02 Peve lncRNA align

Steven Roberts 08 September, 2023

0.0.1 Analysis:
0.0.2 Suggestions:
1 Blast to sRNA, genome, proteome….
- 1.1 lncRNA fasta
2 make some blastdb
3 Blast comparison
4 Result - database: sRNA
5 Result -database: genome
6 Result - database: proteome
7 Result - database: lncRNA

#TLDR

The code and its output suggest that you are running BLAST comparisons on a set of long non-coding RNAs (lncRNAs) against different databases—small RNAs (sRNAs), genome, and proteome—and observing different patterns of hits.

sRNA Database:
- In the first run, you used a stringent e-value (1E-40) and got 0 hits.
- In the second run without e-value restriction, you got 1,798,786 hits.
Genome Database:
- Without an e-value restriction, you got 14,547,262 hits.
- With an e-value restriction of 1E-40, the hits reduced to 26,669.
Proteome Database:
- You got 351,260 hits when querying against the proteome database.

0.0.1 Analysis:

sRNA Database: The 0 hits in the first run suggest that no lncRNAs had significant similarity to sRNAs under the stringent conditions. However, when the stringency was relaxed, a high number of hits were observed. This suggests that there is some level of sequence similarity between lncRNAs and sRNAs, but it may not be functionally relevant (at least under stringent e-value settings).
Genome Database: As expected, you see a vast number of hits when the e-value is not restricted. It narrows down to a more manageable number when stringency is increased, but still, a large number of hits are observed. This could be due to the fact that the lncRNAs are part of the genome, and thus, self-matches and paralogous sequences might be increasing the hits.
Proteome Database: The number of hits suggests that some of these lncRNAs might have regions that could be translated into protein sequences or resemble known proteins, although lncRNAs are generally not translated.

0.0.2 Suggestions:

Analyze Overlap: You could analyze the overlapping hits between these databases to see if any lncRNAs show hits in all three databases.
Functional Annotation: Use other bioinformatic tools to predict the functional roles of the lncRNAs that show significant hits.
Alignment Visualization: You might want to visualize some of these alignments to better understand the areas of similarity.
Statistical Significance: You may also apply statistical tests to see if the number of hits in any of these databases is significantly higher than expected by chance.
Investigate Parameters: Review BLAST parameters like -max_target_seqs and -max_hsps based on your research questions, as these can impact your results.

Remember, the number of hits alone doesn’t convey functional or biological significance; further investigation is needed.

1 Blast to sRNA, genome, proteome….

1.1 lncRNA fasta

head ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta

fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta

## >::Porites_evermani_scaffold_1:422643-423512
## GGCAAAGCCACAATCCATGATAAATGAGGGCATAAGCCCGAGGAAGAAGAACTCATAGATCTTGTCCTAATCCCTTTTGGGAGAGCACATTTTTTTCTTTATGCACTCACTGTGGATAAACACTCAATGGATTTTAGAGAAAAGGTGGACTGTAAGCAGTATAATACCTCCTGGAATTTGCCAGTAACTGAAAGAATCTAATCTGAAAAGTCTCTAGGTGTATACTGGGCAACATAGTAATAATTAGTGCATTTTAGAAGATAGGAATGAACGTGGCACATGTATCAAAATTGCATCTTACAAAATAGTTATATTATCAAGAAATCCCTTGCTAAATAATAATTGTAAATCAAGACATGTTTCTAGAACTGGAAACTCCTGGAAATCTGTATGCATCATGTCAATCACTGTACCAATGTTCCCTCATAGAGGGTTTTATATACTAGAAACACTTTGTGAGACTTAAATGTGTTATGCAATTCCAGGTTTGACTACTGTTCCAGGGTCTCAGTCAGTTAAGATGCAGGCATAAGTGAGAGACAGCCCTCCATTCCTTCCTCTCCCTTTTTTTTGGCACTTGGTTTTCTATTTGCTGAATGCCAGTAACTGAGAGCCTAGAACAACCTAGGTTTATGAAAAGTTTCAAGTAATGCTGATACAACTGTGGGAGTTTTGAACCCAGGAGTCACTTCAAAAGTAGGTTGAGTTTGATCGTCCAGGTGAACGTAGTCCTGAATAGGACTGTTGTTGTTGACAGTGACTGACGTTTCGACAACCTGTGCGGTAGTCATTTTCCTATTCAGGATTCATTCACCCGAACATACTTTTGGAATGCTGATACAGTTAACTATCCTTACACACAAACAATG
## >::Porites_evermani_scaffold_1:1084867-1089422
## AGGGATTAGCTGTTTTTAATTTTTGTGACTTCCAGAGAGTACCCAGTACCCAGCATTGATAATATTTTCGTTTTTATTGAGTATGTGCAATAGTCTAAGATAGAAATACATACTTTCAAACAATACGGTGTGAATACAGTGTGCATGCCCTATGCAAACCAGTATTTCAGTGTATACCATTCTGTTTCTGAACTAGGGGAATGAAACAAGTTGTAACAATTTTGAACAGACACACTTGTGTAGCGAATTTAAGTTAGAGAATATTTACTTCGGAATAAACAATTAAAAAAATAGCAAACATTAGAACCCACAAAAATTTCAGCAAAATAAAATAATAACACAGCAATTAACAATTTTTCATCCTCCAGTCAACTTGTAATTGGCTAATTAAAATGAACAAAACTACCTTTATGAGCATCATGGACACAAATATAGTACTACATGTAACAACAGTATTCTTTTCAATCTCACTGAATAGTGGCCACAAGAATAATAATTATTTTGCTCTATATTCAACGCCTAGCACACTTATTTCAATGCTGTAGTTAGACTGCATATTGCACATCTGATTTGAGAAAATCAACTGGCCCTCATACGGCATCTTTCCTGCTTTTTTCTTTTTCTAGGATATTCACAAGAATGATCCCCATTCCCTTTCAAAAAAGGGAAGGGAAGCAGAGTATAAGCGAAAGACTAGAGGGGAAACAGAGGTTTGAGGCCTTCCTCAGAGCAGCACCGAAAAGTGTGGGTGTTTTTATAAAACTTCATGAAGCATATGAGGAAATGACTAAAAGCCCACTCTTTAAGAACATTGAACAGGAGATCCAACCACTTGATCTTGACGTTCGGTCACAATCAAATTTAGCAGTTCTCCTTTATTCCACTGGCAAGGTACTAATAAAGAACAAAGTAGATAAAAATAATAATTAATACTGTGAAATTCTAAAATGCCCTGGGCCGAGTTGTTCAAAGCTGGGTTAAGATAACCCAGGGTTATTTGAAGAGATTTGAATTCAGATTTGAAAGCTTAAAAAGCATTTCGGTTTAAGTTCTTTGTGTTGACAAGTTGATGATTGGAAGCTCTAAAAATAACAGAGAAAATTTCCGAGAAAATACTTTAGAACACAAGAACAAGAAACCCGGGTTAAATTTAACCCCAGGTTAAGCGCTAACCAGCCTTTGAAGAACTGGGCCCTGGTTACTTTCTACTTAAATAAGCAAAAGGGGCCACTACTTTAAGGTTGTTGTTGTCTTGGGGTAATCATTCCTTTTGGATGGTTAAAAAAAACTTAGTAGTTTTTTTTGAGGGTGGCATTTATTGGTACTTATGCTTCCATGTGTGGCATTTGTTCGAGGGTGGCATTTAATCGAATAATAATAGTTCACAGTTTTAGTCGAGACAGTTTCGCACATATGGTACCATAGTTCACAGATTATGACACATTGAGGCTTTTATTAAATTGATTTGTTACTATGAATGGTGCTAGCTGTGTTTTGGAAAAAAACTTGTTATTATAGTGTAGTTAGAATAAACTTCATCTGGTGTGACTTTAATCCTTTCCTGAACTGAAATTATTTCATCGGAAAGTGTATGAATTTATCACTTTATTATTATCCATGCTGTAAGGATGTGAAACTAAGTCTAAGGAAAAATAATGTATGTCACACCTTCTTTAATTTTGTGTACAATGTTGTTACAGATCTTGGATTATATTGGAATGAAAAACCGGTACTGGGCAGACATACTTCTATTTATAAAAGAAGTTATGGTCCCGAAGTACCAAGCTCTGCTGGTTGGTAACATTGAGAAAATGCAGAACATGTCCTCCAATCAGCAATTCAGTGGCATGGAAGATTCTTGCCTTCAGGCAATTGAACAGATTGTTCGAACTGCCATGGAATACCCAAATAAGGTAAGCGTTTGTATTTTTATTAATCACTATTACATGTATTATTTTAATAAGACATTTACCGGATGGTACATGTAGGTAGTGGACCATGAAGCCCCGGGCGGGGGGAAGGAGTTGGCTAAGGTACATGTAGCCTTCCCCAATGTATGCTCAGTTGTATCTTTAAAGCCTTATTCATGAATAAAAGCACACTAATATTTTAAGATACCAACAAAAATCCAAAGCCCAAGGGTTTAAATTGGGCATCAATTTAGATAAAGATTTCAAGAGATGAAGAGCTAAACTGGTCACAATAGACTGTAATATCCTTAATCTCCTTTGTCTTCCTTCACAGGCCAAAGACTACCTCAAACCTAAAAGTGCAACAACAAGTTGCCTTTGTGGTGAAGTGGTATCCTTCAATGTTCCCCAAGCATTCCAACATGCGGGTATTACTGTTTCTTCTACAATCTTCAGACAGTATATAAAAAAAAAATGAGTTGGGCTGTACTGGAAAAAACATGCACTTACCTAGTGGGAAAAATGTAACTTGCGTCCACCTTAGCCGAGGAAAACTGCCACAAGAAATTCTGGAAATCCTAAACAAAGGTAATTTGATTTTTATTAAGTATTGACGCATTTAACTTAAAGATAAAACTTTGGCATTCTTCTGGCATACCAAAATTTACATCAAACCATTAAACCTTCAATGCATTTACAGCCACAAGCAGCTCTACTACTGTTACCACTTCCTCAGAATCTCTTGATGTTGCACCAGTAATGGAAGCACAAAAGTCAGGTATATAGTGCTATTTTAATTAATTAAACAAAGAAAACAGTGTGGAGACAGAAACGATCCTTCCTTTTCGTATATGTTGTAGTTAATTAATTTTTTTTTTATCTCGGGTAATTTTTATTTTTCCTTTCATAAGAATACATTACCATATCCAAAAACAAAAGAAAAAAAAAGTACCCTGGGCTAAAAAATTAACTACAATAGACACTCTCAACCAATGAAAGTGAAGTCAAGGTGGGTGGTGGACCAGATGAGACAAACACCCAAACATAGAACATGTGGAAATACATGTAACAACAATCAAATCTATTATGAGATCACATTGTTTGTTTAGGATGAAACTAGATGATAAGCAATCTACAAAAATTAGTGCTAGACTAAATTATACATGTATACATGTATAAGAGGTAATGTGCTCAAGGCTGACATTTAATATTTATTATTATTACTAATATTATTATTTGGTAGATAAAATGCATTTAGTTAAGTTAAGTTAAACAGGAAATTAAATGGGCAGTCCAATCTAGTATTTAAAGTAGAATTAAAGATGACAAATTTGGCATTCTTCTGGTATATCAGAATTTATCTTCTGTCTAATAATAACCCTTTTCACCCTGAAATTGTGTTTGCAGCCACCAGTAGCTCTACTACTGTAAAAACCTCCTCAGAATCTCTTAATGCTGCAGAGGTGGTGGAAGTACAAATGTCAGGTAAGAGCTATTCCCCGCTTATACTCTACATATAATAACAAAGATTGCATGTTTGTATCTTAATAATTATTTTTTTACTATTAATAGGCCAGTTCCCCCGGGCCTCTGTTTCAAAACTAGGGTAGGTGCTCAGCCTTTGGTATGGAGATCACTTTTTCATTCTCATGCAAATAAAACTCATTTTCGCAATAAAGGTTGTGCACCCAGCTTCATTTTGAAAGTGAGGGTTTTTGGAGCTCGCAGTTGGCCTATTTTAATGAGAGACAAGATTGTGTGATTATTATGTCACTGCAACCATCCACTGGCATGGCATTGCATGGTCTCTTTTCCTATAACCCTTACTAATTACAGTGGAGTCTCTATTAAAGGGGACACCCTCGGGACCAAGGCAAGAGGAGGTTGGGTTTTTAGTTAATATTGATAAAGGCATAAAATGTTTTCCTTTCATTTTGCCTTAAATCTGCTGTTGCCATAATTTTAAGCAGCTTGATAAAGCATTGCAAAATCATGAATAACAAACGTGTATTTCTGCGATGTTGCATGTTGAATTTCCAAAACTAGTACAATACAAATGATAATTGATGTACGTGAGATAATTCATGATTGACAAGCTGTTGTAATTATGACAAATGTACCCTTAAACTTATCAACAGGTTTCGTGGTCAGTCACTTTTTGTGTGCTAAGTTATCCCCTGAATGGTAAAGAGGTTAAACACAGGTTTTTCCTTTCTAAAAATAGAGGTGTCCCTTCAAGAGAGGTAACAAATAGTAATACAACAAAATATTTACATGTACCTCTCCAATCTTTACCCAGCTGCTGTTGCTTCTAATAATACTGTAGAAGAATCTAACATTGATGCTGAACCTGCAATGGTGGAAAACCAAGTGTCAGGTAAGTAAACAAATTGCTTGTTATAATAGGCCGACATTTTACAGTTATGACTTATGGATGGAAGCGAGAGTGGAGGTGACCTTATTTTGATACAAACCTCCTTCTTTGCCATGAAAATTGTCCTTCAAAAATAATAGTTAGCATAAGAACAACTTGATTCAACTTGAATCCAGTCAATTGTATGAAAGCTACGTAAACATACTCACTTAAGAACAAGGACGCTTTTCCTGGTGAGCCTTTCAGACGCCTTTTTTTTTTTAATTTCAAC
## >::Porites_evermani_scaffold_1:372245-372449
## GCCTTTTCTAGTTCCAGGTTTTAGTCTTTTTCAATAACGTTGGTTGTAAATTTTGTTTTTCCAACCTTTTTAACACTTAGAGTCTATTTGTAAGCCATTTTTATATTGTAAGGCAGGTTTTTTATCTCTGTGAAGCAGAAAACAGGGCATTATTTTTATGGATATACAGTGGAACCTCTCTAATACAGACACCGAAGGGACAGA
## >::Porites_evermani_scaffold_1:683878-684280
## TCTTGACTTTTACTTTTCGCTTTCTCTCCTCCCTTCTTTTTTCGCTTTTCTTGCCTCATTTTTTTTTCTCTTGCTGGGCATTTAGTAGGCTTCATTTTGGTGGGAAGAGTTTTTAGGAAAGCTTTTAGGATCTTAGGATTAGGTGAAAGGAAAGGTAGGTGGGTAATGGAACAAGATTTTCATGGAGATTTTCAGGTCCTTGTCACGTGGTTTTTTGCTTCTTTCTCCGGTGTCCTTGACTGAATTGTGCTCATTCTGGTATGGTTTGAAAGATCTCTTCACTCTGCACAAGTTAGCGAAGAAAGTTGTCCTTGACCGTTAAAACTGATGACGTCACAAAGGGTAGAAAGGACCTGGATCCGCACGGGCGGTTACGGGCGGTTCAGGGGCGAATGGGTTAAG
## >::Porites_evermani_scaffold_1:1202044-1202328
## GGGAGTAGCCTATGGATGAAAACATTTTGAGAACATGGTCAGGCAATGGTTTCGACTCCCTTTGGTCATAGCCTGCTCCAGGCGTTCTGATTGTGGAGCGTGGCGGCGTCGCTGTTTTTCCCGTCCCCACGATCTGAACGCCTGGAACAGGCTACTTTCGGCATTGCTAAACTTCTTACCCACAATTCGCGTTCCGTTTGTTTTTGTTGCTGTTGGCGGTTTTGTTGTTTTTTGTTGATGATGTTGTTGTTTTTTTAGTTCAGAGTGTTTCTCGACGTCTAGCG
## 7018

2 make some blastdb

2.1 sRNA

ls ../../DEF-cross-species/data/blast/peve_sRNA*

## ../../DEF-cross-species/data/blast/peve_sRNA.ndb
## ../../DEF-cross-species/data/blast/peve_sRNA.nhr
## ../../DEF-cross-species/data/blast/peve_sRNA.nin
## ../../DEF-cross-species/data/blast/peve_sRNA.not
## ../../DEF-cross-species/data/blast/peve_sRNA.nsq
## ../../DEF-cross-species/data/blast/peve_sRNA.ntf
## ../../DEF-cross-species/data/blast/peve_sRNA.nto

2.2 Genome

https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa

cd ../data/
curl -O https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa

head ../data/Porites_evermanni_v1.fa

## >Porites_evermani_scaffold_1
## GGCGGGGGGGGGGGGGGGGGGGGTACTCCCATACATTACCTATACGGGTATGTGCCGCCC
## AAAAGGGGCCGTGATTTTGAAGCTCCTGATTTAGAACGGGGTATCCATTTCAGAGGCGTT
## TTCTAGAACGGGGTGTAATATTTCGAACGCACGAAAGCTCCACTTTTGTGTAAGCAGCCA
## TTTGAAATTATTCAAGGACAGATTGCTTTTAAAAATACGGTTCAGCGCGTTAACAAGCAA
## ACCGTTGTACTCTTGTTGCACCCTAGAACGGTGTATAAAAAATTGGCCCATTTCTAGAAC
## GGGGTATCAGTTTTAGGGAGAATTCTAGAACGGGGTATAAAAAATTGGCCCTTTTCTGAA
## CGGGGCATCAATGTTAGGGGAAATTTTTTCCAGAACGGGGTGCCAATTTGGAGTCCCGGG
## CGGCACATACCCACCCAAAAAATACCCAAGTGCCCCCCCGGGGTCTAAACCCACATATTC
## TTCACACTGTTCACAATTTACCTCTTTTGGCTCTTCTAAGGAGAGCTCATCTAAATATTG

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../data/Porites_evermanni_v1.fa \
-dbtype nucl \
-out ../data/blast/pmea_genome

ls ../data/blast/pmea_genome*

## ../data/blast/pmea_genome.ndb
## ../data/blast/pmea_genome.nhr
## ../data/blast/pmea_genome.nin
## ../data/blast/pmea_genome.not
## ../data/blast/pmea_genome.nsq
## ../data/blast/pmea_genome.ntf
## ../data/blast/pmea_genome.nto

2.3 Proteins

https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.pep.fa

cd ../data/

curl -O https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.pep.fa

head ../data/Porites_evermanni_v1.annot.pep.fa

## >Peve_00000001 assembled CDS
## KILADAGAVISGAQLGLGILTTILNTLGSISRKVAIGVDNESGYKWRAVNIYFYSGTSNR
## VLPHDVSSGTALLYGARKTAGPVARGAVGVLTYYIPHIDKTLAVMYSVPFDYNWYSNWFD
## VWLYSGKRRANYNLWYRMYYDNPFKGDNYWHERDLGSGLRARGAMSNSGQATIEIHILKQ
## *
## >Peve_00000002 assembled CDS
## MPSVSRSASPPSSPMSPPRKKTRFSLKLKSKKKASSESDPDKREKLYPIFSPPTAQNASD
## DETCEPPKPPPPYAGLRNHGNICYANAVVQVLRHCPGILESVDELDSLVKEKNYCATEGK
## SFDTRTDGKENGSEDLENCCDQKHVVCELRELFSQMEELEQDYNDNKENCEHLVQRRNTL
## VLAAKPLDFMQTFRGKNPLFEDNLQHDAQEFLCSLLVDLQDTETEIKKKREDPRKMYIGD

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../data/Porites_evermanni_v1.annot.pep.fa \
-dbtype prot \
-out ../data/blast/pmea_proteome

ls ../data/blast/pmea_proteome*

## ../data/blast/pmea_proteome.pdb
## ../data/blast/pmea_proteome.phr
## ../data/blast/pmea_proteome.pin
## ../data/blast/pmea_proteome.pot
## ../data/blast/pmea_proteome.psq
## ../data/blast/pmea_proteome.ptf
## ../data/blast/pmea_proteome.pto

2.4 lncRNA

ls ../../DEF-cross-species/data/blast/peve*lncRNA*

## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.ndb
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nhr
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nin
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.not
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nsq
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.ntf
## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nto

2.5 Genes

???

3 Blast comparison

4 Result - database: sRNA

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_sRNA \
-out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 5 \
-max_hsps 1 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab

## Number of hits?
## 0 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab
## File header

(nothing)

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_sRNA \
-out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab \
-num_threads 20 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab

## Number of hits?
## 1798786 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  1830741-1   100.000 35  0   0   726 760 35  1   3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  1848065-1   100.000 35  0   0   748 782 35  1   3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  907001-1    100.000 35  0   0   261 295 1   35  3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  874194-1    100.000 35  0   0   713 747 1   35  3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  439663-3    100.000 34  0   0   753 786 1   34  1.25e-09    62.6
## ::Porites_evermani_scaffold_1:422643-423512  2530059-1   97.143  35  1   0   723 757 1   35  1.52e-08    59.9
## ::Porites_evermani_scaffold_1:422643-423512  676574-2    97.143  35  1   0   734 768 1   35  1.52e-08    59.9
## ::Porites_evermani_scaffold_1:422643-423512  510681-2    97.143  35  1   0   753 787 1   35  1.52e-08    59.9
## ::Porites_evermani_scaffold_1:422643-423512  535611-2    97.143  35  1   0   737 771 1   35  1.52e-08    59.9
## ::Porites_evermani_scaffold_1:422643-423512  342166-4    97.143  35  1   0   752 786 35  1   1.52e-08    59.9

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_sRNA \
-out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab \
-evalue 1E-08 \
-num_threads 20 \
-outfmt 6

echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab

echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab

## Number of hits?
## 29152 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  1830741-1   100.000 35  0   0   726 760 35  1   3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  1848065-1   100.000 35  0   0   748 782 35  1   3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  907001-1    100.000 35  0   0   261 295 1   35  3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  874194-1    100.000 35  0   0   713 747 1   35  3.58e-10    64.4
## ::Porites_evermani_scaffold_1:422643-423512  439663-3    100.000 34  0   0   753 786 1   34  1.25e-09    62.6
## ::Porites_evermani_scaffold_1:1084867-1089422    2127498-1   100.000 35  0   0   962 996 35  1   7.70e-10    64.4
## ::Porites_evermani_scaffold_1:683878-684280  1639214-1   100.000 35  0   0   222 256 1   35  1.60e-10    64.4
## ::Porites_evermani_scaffold_1:683878-684280  1195174-1   100.000 35  0   0   248 282 1   35  1.60e-10    64.4
## ::Porites_evermani_scaffold_1:683878-684280  1173775-1   100.000 35  0   0   244 278 1   35  1.60e-10    64.4
## ::Porites_evermani_scaffold_1:683878-684280  903402-1    100.000 35  0   0   262 296 1   35  1.60e-10    64.4

5 Result -database: genome

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_genome \
-out ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab \
-num_threads 20 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab

## Number of hits?
## 14547262 ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 100.000 869 0   0   1   869 422644  423512  0.0 1568
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 94.958  119 6   0   663 781 1690031 1690149 7.22e-46    188
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 90.196  102 10  0   694 795 1764562 1764461 3.28e-31    140
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 81.690  142 19  3   657 794 967689  967827  4.87e-29    132
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 84.337  83  9   2   714 795 642727  642806  6.34e-15    86.9
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 87.879  66  5   1   695 760 766442  766504  7.72e-14    82.4
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 87.692  65  5   1   731 795 1340298 1340237 2.69e-13    80.6
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 83.333  72  12  0   663 734 1340494 1340423 3.28e-12    77.0
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 89.091  55  6   0   663 717 1269951 1270005 4.00e-11    73.4
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 80.645  62  9   1   730 791 1333238 1333180 3.07e-06    57.2

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_genome \
-out ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab \
-evalue 1E-40 \
-num_threads 20 \
-max_target_seqs 5 \
-max_hsps 1 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab

## Number of hits?
## 26669 ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1 100.000 869 0   0   1   869 422644  423512  0.0 1568
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_1058  95.035  141 7   0   655 795 26887   27027   3.50e-56    224
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_940   94.366  142 8   0   654 795 11486   11627   1.22e-55    221
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_546   94.444  144 7   1   653 795 161133  160990  1.22e-55    221
## ::Porites_evermani_scaffold_1:422643-423512  Porites_evermani_scaffold_2450  94.964  139 7   0   657 795 5502    5640    4.26e-55    220
## ::Porites_evermani_scaffold_1:1084867-1089422    Porites_evermani_scaffold_1 100.000 4555    0   0   1   4555    1084868 1089422 0.0 8215
## ::Porites_evermani_scaffold_1:1084867-1089422    Porites_evermani_scaffold_1840  85.342  921 100 10  16  932 36761   35872   0.0 1040
## ::Porites_evermani_scaffold_1:1084867-1089422    Porites_evermani_scaffold_1041  90.661  257 21  2   942 1197    52891   52637   1.88e-93    350
## ::Porites_evermani_scaffold_1:1084867-1089422    Porites_evermani_scaffold_705   91.600  250 16  4   955 1201    50079   49832   8.01e-92    343
## ::Porites_evermani_scaffold_1:1084867-1089422    Porites_evermani_scaffold_3651  91.129  248 19  2   953 1199    5737    5982    2.80e-91    343

6 Result - database: proteome

/home/shared/ncbi-blast-2.11.0+/bin/blastx \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_proteome \
-out ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab \
-num_threads 20 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab

## Number of hits?
## 351260 ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00020583   75.000  40  7   2   791 672 1   37  2.36e-04    40.0
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00044132   66.667  27  9   0   740 660 143 169 3.17e-04    41.2
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00030450   60.606  33  12  1   740 642 926 957 4.05e-04    42.4
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00029860   82.609  23  3   1   795 727 113 134 0.002   40.0
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00012851   56.410  39  12  1   791 675 1   34  0.007   37.0
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00000808   50.000  32  16  0   740 645 17  48  0.074   33.9
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00043711   60.870  23  9   0   740 672 95  117 0.15    32.7
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00014361   88.235  17  2   0   663 713 112 128 0.20    33.5
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00010764   77.419  31  7   0   794 702 27  57  0.74    30.4
## ::Porites_evermani_scaffold_1:422643-423512  Peve_00019544   69.048  42  13  0   687 812 698 739 0.86    32.0

/home/shared/ncbi-blast-2.11.0+/bin/blastx \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../data/blast/pmea_proteome \
-out ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab \
-evalue 1E-40 \
-num_threads 20 \
-max_target_seqs 5 \
-max_hsps 1 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab

## Number of hits?
## 1684 ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab
## File header
## ::Porites_evermani_scaffold_10:260427-263111 Peve_00036837   51.678  149 68  3   1525    1965    1   147 5.36e-44    156
## ::Porites_evermani_scaffold_10:260440-263111 Peve_00036837   51.678  149 68  3   1512    1952    1   147 5.30e-44    156
## ::Porites_evermani_scaffold_10:25818-26461   Peve_00041908   52.577  97  42  1   6   296 76  168 1.79e-50    87.0
## ::Porites_evermani_scaffold_1011:155450-155947   Peve_00036185   97.203  143 4   0   452 24  150 292 1.15e-59    187
## ::Porites_evermani_scaffold_1013:148823-153034   Peve_00015807   58.736  269 47  5   3   809 59  263 2.61e-73    245
## ::Porites_evermani_scaffold_1013:148823-153034   Peve_00025583   57.249  269 51  3   3   809 58  262 1.90e-72    243
## ::Porites_evermani_scaffold_1013:148823-153034   Peve_00005800   57.249  269 51  3   3   809 59  263 6.57e-72    241
## ::Porites_evermani_scaffold_1013:148823-153034   Peve_00004106   58.736  269 47  3   3   809 60  264 4.23e-71    239
## ::Porites_evermani_scaffold_1013:148823-153034   Peve_00015805   55.390  269 56  3   3   809 59  263 7.84e-70    235
## ::Porites_evermani_scaffold_1016:8862-9109   Peve_00015308   87.500  80  10  0   2   241 1125    1204    2.38e-42    146

7 Result - database: lncRNA

../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \
-out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab \
-evalue 1E-40 \
-num_threads 20 \
-max_target_seqs 5 \
-max_hsps 1 \
-outfmt 6


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab


echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab

## Number of hits?
## 20675 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_1:422643-423512 100.000 869 0   0   1   869 1   869 0.0 1568
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_6072:1826-3677  93.939  132 8   0   663 794 822 953 8.17e-52    203
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_4084:10-8062    93.077  130 9   0   661 790 3059    2930    4.23e-49    195
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_922:4504-6380   93.701  127 8   0   669 795 777 651 4.23e-49    194
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_542:179250-194358   93.701  127 8   0   669 795 14003   13877   4.23e-49    194
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_1:1084867-1089422   100.000 4555    0   0   1   4555    1   4555    0.0 8215
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_3651:5736-5980  91.057  246 19  2   953 1197    1   244 8.45e-92    339
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_3419:30975-37690    89.879  247 22  2   955 1200    2207    2451    1.53e-88    327
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_1800:46422-47018    89.919  248 21  3   951 1197    229 473 5.33e-88    325
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_4104:26106-31512    88.800  250 24  3   951 1198    3479    3232    9.64e-85    315

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \
-out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab \
-evalue 1E-40 \
-num_threads 20 \
-max_hsps 1 \
-outfmt 6

Note


fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta

## 7018


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab

## Number of hits?
## 130492 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \
-out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab \
-evalue 1E-80 \
-max_hsps 1 \
-num_threads 20 \
-outfmt 6

Note


fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta

## 7018


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab

## Number of hits?
## 52624 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \
-db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \
-out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab \
-evalue 1E-300 \
-num_threads 20 \
-max_hsps 1 \
-outfmt 6

Note


fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta

## 7018


echo "Number of hits?"
wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab

echo "File header"
head ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab

## Number of hits?
## 7189 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab
## File header
## ::Porites_evermani_scaffold_1:422643-423512  ::Porites_evermani_scaffold_1:422643-423512 100.000 869 0   0   1   869 1   869 0.0 1568
## ::Porites_evermani_scaffold_1:1084867-1089422    ::Porites_evermani_scaffold_1:1084867-1089422   100.000 4555    0   0   1   4555    1   4555    0.0 8215
## ::Porites_evermani_scaffold_10:260427-263111 ::Porites_evermani_scaffold_10:260427-263111    100.000 2684    0   0   1   2684    1   2684    0.0 4841
## ::Porites_evermani_scaffold_10:260427-263111 ::Porites_evermani_scaffold_10:260440-263111    100.000 2671    0   0   14  2684    1   2671    0.0 4818
## ::Porites_evermani_scaffold_10:260440-263111 ::Porites_evermani_scaffold_10:260440-263111    100.000 2671    0   0   1   2671    1   2671    0.0 4818
## ::Porites_evermani_scaffold_10:260440-263111 ::Porites_evermani_scaffold_10:260427-263111    100.000 2671    0   0   1   2671    14  2684    0.0 4818
## ::Porites_evermani_scaffold_10:890033-892111 ::Porites_evermani_scaffold_10:890033-892111    100.000 2078    0   0   1   2078    1   2078    0.0 3748
## ::Porites_evermani_scaffold_10:1071612-1085055   ::Porites_evermani_scaffold_10:1071612-1085055  100.000 13443   0   0   1   13443   1   13443   0.0 24243
## ::Porites_evermani_scaffold_10:1071612-1085055   ::Porites_evermani_scaffold_10:1071808-1085055  100.000 13247   0   0   197 13443   1   13247   0.0 23890
## ::Porites_evermani_scaffold_10:1071612-1085055   ::Porites_evermani_scaffold_10:1075979-1085055  100.000 9076    0   0   4368    13443   1   9076    0.0 16368

--- title: "Peve lncRNA alignment" description: "" author: - name: Steven Roberts url: https://sr320.github.io/ orcid: 0000-0001-8302-1138 affiliation: Professor, UW - School of Aquatic and Fishery Sciences affiliation-url: https://robertslab.info date: 09-08-2023 categories: [deepdive, R, lncrna, e5] # self-defined categories #citation: #url: # self-defined image: http://gannet.fish.washington.edu/seashell/snaps/2023-09-12_08-31-07.png # finding a good image draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! format: html: code-fold: true code-tools: true code-copy: true highlight-style: github code-overflow: wrap --- 02 Peve lncRNA align ================ Steven Roberts 08 September, 2023 - <a href="#001-analysis" id="toc-001-analysis">0.0.1 Analysis:</a> - <a href="#002-suggestions" id="toc-002-suggestions">0.0.2 Suggestions:</a> - <a href="#1-blast-to-srna-genome-proteome" id="toc-1-blast-to-srna-genome-proteome">1 Blast to sRNA, genome, proteome….</a> - <a href="#11-lncrna-fasta" id="toc-11-lncrna-fasta">1.1 lncRNA fasta</a> - <a href="#2-make-some-blastdb" id="toc-2-make-some-blastdb">2 make some blastdb</a> - <a href="#21-srna" id="toc-21-srna">2.1 sRNA</a> - <a href="#22-genome" id="toc-22-genome">2.2 Genome</a> - <a href="#23-proteins" id="toc-23-proteins">2.3 Proteins</a> - <a href="#24-lncrna" id="toc-24-lncrna">2.4 lncRNA</a> - <a href="#25-genes" id="toc-25-genes">2.5 Genes</a> - <a href="#3-blast-comparison" id="toc-3-blast-comparison">3 Blast comparison</a> - <a href="#4-result---database-srna" id="toc-4-result---database-srna">4 Result - database: sRNA</a> - <a href="#5-result--database-genome" id="toc-5-result--database-genome">5 Result -database: genome</a> - <a href="#6-result---database-proteome" id="toc-6-result---database-proteome">6 Result - database: proteome</a> - <a href="#7-result---database-lncrna" id="toc-7-result---database-lncrna">7 Result - database: lncRNA</a> \#TLDR The code and its output suggest that you are running BLAST comparisons on a set of long non-coding RNAs (lncRNAs) against different databases—small RNAs (sRNAs), genome, and proteome—and observing different patterns of hits. 1. **sRNA Database**: - In the first run, you used a stringent e-value (1E-40) and got 0 hits. - In the second run without e-value restriction, you got 1,798,786 hits. 2. **Genome Database**: - Without an e-value restriction, you got 14,547,262 hits. - With an e-value restriction of 1E-40, the hits reduced to 26,669. 3. **Proteome Database**: - You got 351,260 hits when querying against the proteome database. ### 0.0.1 Analysis: - **sRNA Database**: The 0 hits in the first run suggest that no lncRNAs had significant similarity to sRNAs under the stringent conditions. However, when the stringency was relaxed, a high number of hits were observed. This suggests that there is some level of sequence similarity between lncRNAs and sRNAs, but it may not be functionally relevant (at least under stringent e-value settings). - **Genome Database**: As expected, you see a vast number of hits when the e-value is not restricted. It narrows down to a more manageable number when stringency is increased, but still, a large number of hits are observed. This could be due to the fact that the lncRNAs are part of the genome, and thus, self-matches and paralogous sequences might be increasing the hits. - **Proteome Database**: The number of hits suggests that some of these lncRNAs might have regions that could be translated into protein sequences or resemble known proteins, although lncRNAs are generally not translated. ### 0.0.2 Suggestions: 1. **Analyze Overlap**: You could analyze the overlapping hits between these databases to see if any lncRNAs show hits in all three databases. 2. **Functional Annotation**: Use other bioinformatic tools to predict the functional roles of the lncRNAs that show significant hits. 3. **Alignment Visualization**: You might want to visualize some of these alignments to better understand the areas of similarity. 4. **Statistical Significance**: You may also apply statistical tests to see if the number of hits in any of these databases is significantly higher than expected by chance. 5. **Investigate Parameters**: Review BLAST parameters like `-max_target_seqs` and `-max_hsps` based on your research questions, as these can impact your results. Remember, the number of hits alone doesn’t convey functional or biological significance; further investigation is needed. # 1 Blast to sRNA, genome, proteome…. ## 1.1 lncRNA fasta ``` bash head ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta ``` ## >::Porites_evermani_scaffold_1:422643-423512 ## GGCAAAGCCACAATCCATGATAAATGAGGGCATAAGCCCGAGGAAGAAGAACTCATAGATCTTGTCCTAATCCCTTTTGGGAGAGCACATTTTTTTCTTTATGCACTCACTGTGGATAAACACTCAATGGATTTTAGAGAAAAGGTGGACTGTAAGCAGTATAATACCTCCTGGAATTTGCCAGTAACTGAAAGAATCTAATCTGAAAAGTCTCTAGGTGTATACTGGGCAACATAGTAATAATTAGTGCATTTTAGAAGATAGGAATGAACGTGGCACATGTATCAAAATTGCATCTTACAAAATAGTTATATTATCAAGAAATCCCTTGCTAAATAATAATTGTAAATCAAGACATGTTTCTAGAACTGGAAACTCCTGGAAATCTGTATGCATCATGTCAATCACTGTACCAATGTTCCCTCATAGAGGGTTTTATATACTAGAAACACTTTGTGAGACTTAAATGTGTTATGCAATTCCAGGTTTGACTACTGTTCCAGGGTCTCAGTCAGTTAAGATGCAGGCATAAGTGAGAGACAGCCCTCCATTCCTTCCTCTCCCTTTTTTTTGGCACTTGGTTTTCTATTTGCTGAATGCCAGTAACTGAGAGCCTAGAACAACCTAGGTTTATGAAAAGTTTCAAGTAATGCTGATACAACTGTGGGAGTTTTGAACCCAGGAGTCACTTCAAAAGTAGGTTGAGTTTGATCGTCCAGGTGAACGTAGTCCTGAATAGGACTGTTGTTGTTGACAGTGACTGACGTTTCGACAACCTGTGCGGTAGTCATTTTCCTATTCAGGATTCATTCACCCGAACATACTTTTGGAATGCTGATACAGTTAACTATCCTTACACACAAACAATG ## >::Porites_evermani_scaffold_1:1084867-1089422 ## AGGGATTAGCTGTTTTTAATTTTTGTGACTTCCAGAGAGTACCCAGTACCCAGCATTGATAATATTTTCGTTTTTATTGAGTATGTGCAATAGTCTAAGATAGAAATACATACTTTCAAACAATACGGTGTGAATACAGTGTGCATGCCCTATGCAAACCAGTATTTCAGTGTATACCATTCTGTTTCTGAACTAGGGGAATGAAACAAGTTGTAACAATTTTGAACAGACACACTTGTGTAGCGAATTTAAGTTAGAGAATATTTACTTCGGAATAAACAATTAAAAAAATAGCAAACATTAGAACCCACAAAAATTTCAGCAAAATAAAATAATAACACAGCAATTAACAATTTTTCATCCTCCAGTCAACTTGTAATTGGCTAATTAAAATGAACAAAACTACCTTTATGAGCATCATGGACACAAATATAGTACTACATGTAACAACAGTATTCTTTTCAATCTCACTGAATAGTGGCCACAAGAATAATAATTATTTTGCTCTATATTCAACGCCTAGCACACTTATTTCAATGCTGTAGTTAGACTGCATATTGCACATCTGATTTGAGAAAATCAACTGGCCCTCATACGGCATCTTTCCTGCTTTTTTCTTTTTCTAGGATATTCACAAGAATGATCCCCATTCCCTTTCAAAAAAGGGAAGGGAAGCAGAGTATAAGCGAAAGACTAGAGGGGAAACAGAGGTTTGAGGCCTTCCTCAGAGCAGCACCGAAAAGTGTGGGTGTTTTTATAAAACTTCATGAAGCATATGAGGAAATGACTAAAAGCCCACTCTTTAAGAACATTGAACAGGAGATCCAACCACTTGATCTTGACGTTCGGTCACAATCAAATTTAGCAGTTCTCCTTTATTCCACTGGCAAGGTACTAATAAAGAACAAAGTAGATAAAAATAATAATTAATACTGTGAAATTCTAAAATGCCCTGGGCCGAGTTGTTCAAAGCTGGGTTAAGATAACCCAGGGTTATTTGAAGAGATTTGAATTCAGATTTGAAAGCTTAAAAAGCATTTCGGTTTAAGTTCTTTGTGTTGACAAGTTGATGATTGGAAGCTCTAAAAATAACAGAGAAAATTTCCGAGAAAATACTTTAGAACACAAGAACAAGAAACCCGGGTTAAATTTAACCCCAGGTTAAGCGCTAACCAGCCTTTGAAGAACTGGGCCCTGGTTACTTTCTACTTAAATAAGCAAAAGGGGCCACTACTTTAAGGTTGTTGTTGTCTTGGGGTAATCATTCCTTTTGGATGGTTAAAAAAAACTTAGTAGTTTTTTTTGAGGGTGGCATTTATTGGTACTTATGCTTCCATGTGTGGCATTTGTTCGAGGGTGGCATTTAATCGAATAATAATAGTTCACAGTTTTAGTCGAGACAGTTTCGCACATATGGTACCATAGTTCACAGATTATGACACATTGAGGCTTTTATTAAATTGATTTGTTACTATGAATGGTGCTAGCTGTGTTTTGGAAAAAAACTTGTTATTATAGTGTAGTTAGAATAAACTTCATCTGGTGTGACTTTAATCCTTTCCTGAACTGAAATTATTTCATCGGAAAGTGTATGAATTTATCACTTTATTATTATCCATGCTGTAAGGATGTGAAACTAAGTCTAAGGAAAAATAATGTATGTCACACCTTCTTTAATTTTGTGTACAATGTTGTTACAGATCTTGGATTATATTGGAATGAAAAACCGGTACTGGGCAGACATACTTCTATTTATAAAAGAAGTTATGGTCCCGAAGTACCAAGCTCTGCTGGTTGGTAACATTGAGAAAATGCAGAACATGTCCTCCAATCAGCAATTCAGTGGCATGGAAGATTCTTGCCTTCAGGCAATTGAACAGATTGTTCGAACTGCCATGGAATACCCAAATAAGGTAAGCGTTTGTATTTTTATTAATCACTATTACATGTATTATTTTAATAAGACATTTACCGGATGGTACATGTAGGTAGTGGACCATGAAGCCCCGGGCGGGGGGAAGGAGTTGGCTAAGGTACATGTAGCCTTCCCCAATGTATGCTCAGTTGTATCTTTAAAGCCTTATTCATGAATAAAAGCACACTAATATTTTAAGATACCAACAAAAATCCAAAGCCCAAGGGTTTAAATTGGGCATCAATTTAGATAAAGATTTCAAGAGATGAAGAGCTAAACTGGTCACAATAGACTGTAATATCCTTAATCTCCTTTGTCTTCCTTCACAGGCCAAAGACTACCTCAAACCTAAAAGTGCAACAACAAGTTGCCTTTGTGGTGAAGTGGTATCCTTCAATGTTCCCCAAGCATTCCAACATGCGGGTATTACTGTTTCTTCTACAATCTTCAGACAGTATATAAAAAAAAAATGAGTTGGGCTGTACTGGAAAAAACATGCACTTACCTAGTGGGAAAAATGTAACTTGCGTCCACCTTAGCCGAGGAAAACTGCCACAAGAAATTCTGGAAATCCTAAACAAAGGTAATTTGATTTTTATTAAGTATTGACGCATTTAACTTAAAGATAAAACTTTGGCATTCTTCTGGCATACCAAAATTTACATCAAACCATTAAACCTTCAATGCATTTACAGCCACAAGCAGCTCTACTACTGTTACCACTTCCTCAGAATCTCTTGATGTTGCACCAGTAATGGAAGCACAAAAGTCAGGTATATAGTGCTATTTTAATTAATTAAACAAAGAAAACAGTGTGGAGACAGAAACGATCCTTCCTTTTCGTATATGTTGTAGTTAATTAATTTTTTTTTTATCTCGGGTAATTTTTATTTTTCCTTTCATAAGAATACATTACCATATCCAAAAACAAAAGAAAAAAAAAGTACCCTGGGCTAAAAAATTAACTACAATAGACACTCTCAACCAATGAAAGTGAAGTCAAGGTGGGTGGTGGACCAGATGAGACAAACACCCAAACATAGAACATGTGGAAATACATGTAACAACAATCAAATCTATTATGAGATCACATTGTTTGTTTAGGATGAAACTAGATGATAAGCAATCTACAAAAATTAGTGCTAGACTAAATTATACATGTATACATGTATAAGAGGTAATGTGCTCAAGGCTGACATTTAATATTTATTATTATTACTAATATTATTATTTGGTAGATAAAATGCATTTAGTTAAGTTAAGTTAAACAGGAAATTAAATGGGCAGTCCAATCTAGTATTTAAAGTAGAATTAAAGATGACAAATTTGGCATTCTTCTGGTATATCAGAATTTATCTTCTGTCTAATAATAACCCTTTTCACCCTGAAATTGTGTTTGCAGCCACCAGTAGCTCTACTACTGTAAAAACCTCCTCAGAATCTCTTAATGCTGCAGAGGTGGTGGAAGTACAAATGTCAGGTAAGAGCTATTCCCCGCTTATACTCTACATATAATAACAAAGATTGCATGTTTGTATCTTAATAATTATTTTTTTACTATTAATAGGCCAGTTCCCCCGGGCCTCTGTTTCAAAACTAGGGTAGGTGCTCAGCCTTTGGTATGGAGATCACTTTTTCATTCTCATGCAAATAAAACTCATTTTCGCAATAAAGGTTGTGCACCCAGCTTCATTTTGAAAGTGAGGGTTTTTGGAGCTCGCAGTTGGCCTATTTTAATGAGAGACAAGATTGTGTGATTATTATGTCACTGCAACCATCCACTGGCATGGCATTGCATGGTCTCTTTTCCTATAACCCTTACTAATTACAGTGGAGTCTCTATTAAAGGGGACACCCTCGGGACCAAGGCAAGAGGAGGTTGGGTTTTTAGTTAATATTGATAAAGGCATAAAATGTTTTCCTTTCATTTTGCCTTAAATCTGCTGTTGCCATAATTTTAAGCAGCTTGATAAAGCATTGCAAAATCATGAATAACAAACGTGTATTTCTGCGATGTTGCATGTTGAATTTCCAAAACTAGTACAATACAAATGATAATTGATGTACGTGAGATAATTCATGATTGACAAGCTGTTGTAATTATGACAAATGTACCCTTAAACTTATCAACAGGTTTCGTGGTCAGTCACTTTTTGTGTGCTAAGTTATCCCCTGAATGGTAAAGAGGTTAAACACAGGTTTTTCCTTTCTAAAAATAGAGGTGTCCCTTCAAGAGAGGTAACAAATAGTAATACAACAAAATATTTACATGTACCTCTCCAATCTTTACCCAGCTGCTGTTGCTTCTAATAATACTGTAGAAGAATCTAACATTGATGCTGAACCTGCAATGGTGGAAAACCAAGTGTCAGGTAAGTAAACAAATTGCTTGTTATAATAGGCCGACATTTTACAGTTATGACTTATGGATGGAAGCGAGAGTGGAGGTGACCTTATTTTGATACAAACCTCCTTCTTTGCCATGAAAATTGTCCTTCAAAAATAATAGTTAGCATAAGAACAACTTGATTCAACTTGAATCCAGTCAATTGTATGAAAGCTACGTAAACATACTCACTTAAGAACAAGGACGCTTTTCCTGGTGAGCCTTTCAGACGCCTTTTTTTTTTTAATTTCAAC ## >::Porites_evermani_scaffold_1:372245-372449 ## GCCTTTTCTAGTTCCAGGTTTTAGTCTTTTTCAATAACGTTGGTTGTAAATTTTGTTTTTCCAACCTTTTTAACACTTAGAGTCTATTTGTAAGCCATTTTTATATTGTAAGGCAGGTTTTTTATCTCTGTGAAGCAGAAAACAGGGCATTATTTTTATGGATATACAGTGGAACCTCTCTAATACAGACACCGAAGGGACAGA ## >::Porites_evermani_scaffold_1:683878-684280 ## TCTTGACTTTTACTTTTCGCTTTCTCTCCTCCCTTCTTTTTTCGCTTTTCTTGCCTCATTTTTTTTTCTCTTGCTGGGCATTTAGTAGGCTTCATTTTGGTGGGAAGAGTTTTTAGGAAAGCTTTTAGGATCTTAGGATTAGGTGAAAGGAAAGGTAGGTGGGTAATGGAACAAGATTTTCATGGAGATTTTCAGGTCCTTGTCACGTGGTTTTTTGCTTCTTTCTCCGGTGTCCTTGACTGAATTGTGCTCATTCTGGTATGGTTTGAAAGATCTCTTCACTCTGCACAAGTTAGCGAAGAAAGTTGTCCTTGACCGTTAAAACTGATGACGTCACAAAGGGTAGAAAGGACCTGGATCCGCACGGGCGGTTACGGGCGGTTCAGGGGCGAATGGGTTAAG ## >::Porites_evermani_scaffold_1:1202044-1202328 ## GGGAGTAGCCTATGGATGAAAACATTTTGAGAACATGGTCAGGCAATGGTTTCGACTCCCTTTGGTCATAGCCTGCTCCAGGCGTTCTGATTGTGGAGCGTGGCGGCGTCGCTGTTTTTCCCGTCCCCACGATCTGAACGCCTGGAACAGGCTACTTTCGGCATTGCTAAACTTCTTACCCACAATTCGCGTTCCGTTTGTTTTTGTTGCTGTTGGCGGTTTTGTTGTTTTTTGTTGATGATGTTGTTGTTTTTTTAGTTCAGAGTGTTTCTCGACGTCTAGCG ## 7018 # 2 make some blastdb ## 2.1 sRNA ``` bash ls ../../DEF-cross-species/data/blast/peve_sRNA* ``` ## ../../DEF-cross-species/data/blast/peve_sRNA.ndb ## ../../DEF-cross-species/data/blast/peve_sRNA.nhr ## ../../DEF-cross-species/data/blast/peve_sRNA.nin ## ../../DEF-cross-species/data/blast/peve_sRNA.not ## ../../DEF-cross-species/data/blast/peve_sRNA.nsq ## ../../DEF-cross-species/data/blast/peve_sRNA.ntf ## ../../DEF-cross-species/data/blast/peve_sRNA.nto ## 2.2 Genome <https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa> ``` bash cd ../data/ curl -O https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa ``` ``` bash head ../data/Porites_evermanni_v1.fa ``` ## >Porites_evermani_scaffold_1 ## GGCGGGGGGGGGGGGGGGGGGGGTACTCCCATACATTACCTATACGGGTATGTGCCGCCC ## AAAAGGGGCCGTGATTTTGAAGCTCCTGATTTAGAACGGGGTATCCATTTCAGAGGCGTT ## TTCTAGAACGGGGTGTAATATTTCGAACGCACGAAAGCTCCACTTTTGTGTAAGCAGCCA ## TTTGAAATTATTCAAGGACAGATTGCTTTTAAAAATACGGTTCAGCGCGTTAACAAGCAA ## ACCGTTGTACTCTTGTTGCACCCTAGAACGGTGTATAAAAAATTGGCCCATTTCTAGAAC ## GGGGTATCAGTTTTAGGGAGAATTCTAGAACGGGGTATAAAAAATTGGCCCTTTTCTGAA ## CGGGGCATCAATGTTAGGGGAAATTTTTTCCAGAACGGGGTGCCAATTTGGAGTCCCGGG ## CGGCACATACCCACCCAAAAAATACCCAAGTGCCCCCCCGGGGTCTAAACCCACATATTC ## TTCACACTGTTCACAATTTACCTCTTTTGGCTCTTCTAAGGAGAGCTCATCTAAATATTG ``` bash /home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \ -in ../data/Porites_evermanni_v1.fa \ -dbtype nucl \ -out ../data/blast/pmea_genome ``` ``` bash ls ../data/blast/pmea_genome* ``` ## ../data/blast/pmea_genome.ndb ## ../data/blast/pmea_genome.nhr ## ../data/blast/pmea_genome.nin ## ../data/blast/pmea_genome.not ## ../data/blast/pmea_genome.nsq ## ../data/blast/pmea_genome.ntf ## ../data/blast/pmea_genome.nto ## 2.3 Proteins <https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.pep.fa> ``` bash cd ../data/ curl -O https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.annot.pep.fa ``` ``` bash head ../data/Porites_evermanni_v1.annot.pep.fa ``` ## >Peve_00000001 assembled CDS ## KILADAGAVISGAQLGLGILTTILNTLGSISRKVAIGVDNESGYKWRAVNIYFYSGTSNR ## VLPHDVSSGTALLYGARKTAGPVARGAVGVLTYYIPHIDKTLAVMYSVPFDYNWYSNWFD ## VWLYSGKRRANYNLWYRMYYDNPFKGDNYWHERDLGSGLRARGAMSNSGQATIEIHILKQ ## * ## >Peve_00000002 assembled CDS ## MPSVSRSASPPSSPMSPPRKKTRFSLKLKSKKKASSESDPDKREKLYPIFSPPTAQNASD ## DETCEPPKPPPPYAGLRNHGNICYANAVVQVLRHCPGILESVDELDSLVKEKNYCATEGK ## SFDTRTDGKENGSEDLENCCDQKHVVCELRELFSQMEELEQDYNDNKENCEHLVQRRNTL ## VLAAKPLDFMQTFRGKNPLFEDNLQHDAQEFLCSLLVDLQDTETEIKKKREDPRKMYIGD ``` bash /home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \ -in ../data/Porites_evermanni_v1.annot.pep.fa \ -dbtype prot \ -out ../data/blast/pmea_proteome ``` ``` bash ls ../data/blast/pmea_proteome* ``` ## ../data/blast/pmea_proteome.pdb ## ../data/blast/pmea_proteome.phr ## ../data/blast/pmea_proteome.pin ## ../data/blast/pmea_proteome.pot ## ../data/blast/pmea_proteome.psq ## ../data/blast/pmea_proteome.ptf ## ../data/blast/pmea_proteome.pto ## 2.4 lncRNA ``` bash ls ../../DEF-cross-species/data/blast/peve*lncRNA* ``` ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.ndb ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nhr ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nin ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.not ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nsq ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.ntf ## ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs.nto ## 2.5 Genes ??? # 3 Blast comparison # 4 Result - database: sRNA ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_sRNA \ -out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab \ -evalue 1E-40 \ -num_threads 40 \ -max_target_seqs 5 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab ``` ## Number of hits? ## 0 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn.tab ## File header (nothing) ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_sRNA \ -out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab \ -num_threads 20 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab ``` ## Number of hits? ## 1798786 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn02.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 1830741-1 100.000 35 0 0 726 760 35 1 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 1848065-1 100.000 35 0 0 748 782 35 1 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 907001-1 100.000 35 0 0 261 295 1 35 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 874194-1 100.000 35 0 0 713 747 1 35 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 439663-3 100.000 34 0 0 753 786 1 34 1.25e-09 62.6 ## ::Porites_evermani_scaffold_1:422643-423512 2530059-1 97.143 35 1 0 723 757 1 35 1.52e-08 59.9 ## ::Porites_evermani_scaffold_1:422643-423512 676574-2 97.143 35 1 0 734 768 1 35 1.52e-08 59.9 ## ::Porites_evermani_scaffold_1:422643-423512 510681-2 97.143 35 1 0 753 787 1 35 1.52e-08 59.9 ## ::Porites_evermani_scaffold_1:422643-423512 535611-2 97.143 35 1 0 737 771 1 35 1.52e-08 59.9 ## ::Porites_evermani_scaffold_1:422643-423512 342166-4 97.143 35 1 0 752 786 35 1 1.52e-08 59.9 ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_sRNA \ -out ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab \ -evalue 1E-08 \ -num_threads 20 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab ``` ## Number of hits? ## 29152 ../output/02-Peve-lncRNA-align/lncRNA_sRNA_blastn03.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 1830741-1 100.000 35 0 0 726 760 35 1 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 1848065-1 100.000 35 0 0 748 782 35 1 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 907001-1 100.000 35 0 0 261 295 1 35 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 874194-1 100.000 35 0 0 713 747 1 35 3.58e-10 64.4 ## ::Porites_evermani_scaffold_1:422643-423512 439663-3 100.000 34 0 0 753 786 1 34 1.25e-09 62.6 ## ::Porites_evermani_scaffold_1:1084867-1089422 2127498-1 100.000 35 0 0 962 996 35 1 7.70e-10 64.4 ## ::Porites_evermani_scaffold_1:683878-684280 1639214-1 100.000 35 0 0 222 256 1 35 1.60e-10 64.4 ## ::Porites_evermani_scaffold_1:683878-684280 1195174-1 100.000 35 0 0 248 282 1 35 1.60e-10 64.4 ## ::Porites_evermani_scaffold_1:683878-684280 1173775-1 100.000 35 0 0 244 278 1 35 1.60e-10 64.4 ## ::Porites_evermani_scaffold_1:683878-684280 903402-1 100.000 35 0 0 262 296 1 35 1.60e-10 64.4 # 5 Result -database: genome ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../data/blast/pmea_genome \ -out ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab \ -num_threads 20 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab ``` ## Number of hits? ## 14547262 ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 100.000 869 0 0 1 869 422644 423512 0.0 1568 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 94.958 119 6 0 663 781 1690031 1690149 7.22e-46 188 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 90.196 102 10 0 694 795 1764562 1764461 3.28e-31 140 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 81.690 142 19 3 657 794 967689 967827 4.87e-29 132 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 84.337 83 9 2 714 795 642727 642806 6.34e-15 86.9 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 87.879 66 5 1 695 760 766442 766504 7.72e-14 82.4 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 87.692 65 5 1 731 795 1340298 1340237 2.69e-13 80.6 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 83.333 72 12 0 663 734 1340494 1340423 3.28e-12 77.0 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 89.091 55 6 0 663 717 1269951 1270005 4.00e-11 73.4 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 80.645 62 9 1 730 791 1333238 1333180 3.07e-06 57.2 ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../data/blast/pmea_genome \ -out ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab \ -evalue 1E-40 \ -num_threads 20 \ -max_target_seqs 5 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab ``` ## Number of hits? ## 26669 ../output/02-Peve-lncRNA-align/lncRNA_genome_blastn02.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1 100.000 869 0 0 1 869 422644 423512 0.0 1568 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_1058 95.035 141 7 0 655 795 26887 27027 3.50e-56 224 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_940 94.366 142 8 0 654 795 11486 11627 1.22e-55 221 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_546 94.444 144 7 1 653 795 161133 160990 1.22e-55 221 ## ::Porites_evermani_scaffold_1:422643-423512 Porites_evermani_scaffold_2450 94.964 139 7 0 657 795 5502 5640 4.26e-55 220 ## ::Porites_evermani_scaffold_1:1084867-1089422 Porites_evermani_scaffold_1 100.000 4555 0 0 1 4555 1084868 1089422 0.0 8215 ## ::Porites_evermani_scaffold_1:1084867-1089422 Porites_evermani_scaffold_1840 85.342 921 100 10 16 932 36761 35872 0.0 1040 ## ::Porites_evermani_scaffold_1:1084867-1089422 Porites_evermani_scaffold_1041 90.661 257 21 2 942 1197 52891 52637 1.88e-93 350 ## ::Porites_evermani_scaffold_1:1084867-1089422 Porites_evermani_scaffold_705 91.600 250 16 4 955 1201 50079 49832 8.01e-92 343 ## ::Porites_evermani_scaffold_1:1084867-1089422 Porites_evermani_scaffold_3651 91.129 248 19 2 953 1199 5737 5982 2.80e-91 343 # 6 Result - database: proteome ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastx \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../data/blast/pmea_proteome \ -out ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab \ -num_threads 20 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab ``` ## Number of hits? ## 351260 ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00020583 75.000 40 7 2 791 672 1 37 2.36e-04 40.0 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00044132 66.667 27 9 0 740 660 143 169 3.17e-04 41.2 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00030450 60.606 33 12 1 740 642 926 957 4.05e-04 42.4 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00029860 82.609 23 3 1 795 727 113 134 0.002 40.0 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00012851 56.410 39 12 1 791 675 1 34 0.007 37.0 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00000808 50.000 32 16 0 740 645 17 48 0.074 33.9 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00043711 60.870 23 9 0 740 672 95 117 0.15 32.7 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00014361 88.235 17 2 0 663 713 112 128 0.20 33.5 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00010764 77.419 31 7 0 794 702 27 57 0.74 30.4 ## ::Porites_evermani_scaffold_1:422643-423512 Peve_00019544 69.048 42 13 0 687 812 698 739 0.86 32.0 ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastx \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../data/blast/pmea_proteome \ -out ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab \ -evalue 1E-40 \ -num_threads 20 \ -max_target_seqs 5 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab ``` ## Number of hits? ## 1684 ../output/02-Peve-lncRNA-align/lncRNA_proteome_blastx02.tab ## File header ## ::Porites_evermani_scaffold_10:260427-263111 Peve_00036837 51.678 149 68 3 1525 1965 1 147 5.36e-44 156 ## ::Porites_evermani_scaffold_10:260440-263111 Peve_00036837 51.678 149 68 3 1512 1952 1 147 5.30e-44 156 ## ::Porites_evermani_scaffold_10:25818-26461 Peve_00041908 52.577 97 42 1 6 296 76 168 1.79e-50 87.0 ## ::Porites_evermani_scaffold_1011:155450-155947 Peve_00036185 97.203 143 4 0 452 24 150 292 1.15e-59 187 ## ::Porites_evermani_scaffold_1013:148823-153034 Peve_00015807 58.736 269 47 5 3 809 59 263 2.61e-73 245 ## ::Porites_evermani_scaffold_1013:148823-153034 Peve_00025583 57.249 269 51 3 3 809 58 262 1.90e-72 243 ## ::Porites_evermani_scaffold_1013:148823-153034 Peve_00005800 57.249 269 51 3 3 809 59 263 6.57e-72 241 ## ::Porites_evermani_scaffold_1013:148823-153034 Peve_00004106 58.736 269 47 3 3 809 60 264 4.23e-71 239 ## ::Porites_evermani_scaffold_1013:148823-153034 Peve_00015805 55.390 269 56 3 3 809 59 263 7.84e-70 235 ## ::Porites_evermani_scaffold_1016:8862-9109 Peve_00015308 87.500 80 10 0 2 241 1125 1204 2.38e-42 146 # 7 Result - database: lncRNA ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \ -out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab \ -evalue 1E-40 \ -num_threads 20 \ -max_target_seqs 5 \ -max_hsps 1 \ -outfmt 6 ``` ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab ``` ## Number of hits? ## 20675 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_1:422643-423512 100.000 869 0 0 1 869 1 869 0.0 1568 ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_6072:1826-3677 93.939 132 8 0 663 794 822 953 8.17e-52 203 ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_4084:10-8062 93.077 130 9 0 661 790 3059 2930 4.23e-49 195 ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_922:4504-6380 93.701 127 8 0 669 795 777 651 4.23e-49 194 ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_542:179250-194358 93.701 127 8 0 669 795 14003 13877 4.23e-49 194 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_1:1084867-1089422 100.000 4555 0 0 1 4555 1 4555 0.0 8215 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_3651:5736-5980 91.057 246 19 2 953 1197 1 244 8.45e-92 339 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_3419:30975-37690 89.879 247 22 2 955 1200 2207 2451 1.53e-88 327 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_1800:46422-47018 89.919 248 21 3 951 1197 229 473 5.33e-88 325 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_4104:26106-31512 88.800 250 24 3 951 1198 3479 3232 9.64e-85 315 ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \ -out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab \ -evalue 1E-40 \ -num_threads 20 \ -max_hsps 1 \ -outfmt 6 ``` Note ``` bash fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta ``` ## 7018 ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab ``` ## Number of hits? ## 130492 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn02.tab ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \ -out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab \ -evalue 1E-80 \ -max_hsps 1 \ -num_threads 20 \ -outfmt 6 ``` Note ``` bash fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta ``` ## 7018 ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab ``` ## Number of hits? ## 52624 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn03.tab ``` bash /home/shared/ncbi-blast-2.11.0+/bin/blastn \ -task blastn \ -query ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta \ -db ../../DEF-cross-species/data/blast/peve_bedtools_lncRNAs \ -out ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab \ -evalue 1E-300 \ -num_threads 20 \ -max_hsps 1 \ -outfmt 6 ``` Note ``` bash fgrep ">" -c ../../DEF-cross-species/data/peve_bedtools_lncRNAs.fasta ``` ## 7018 ``` bash echo "Number of hits?" wc -l ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab echo "File header" head ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab ``` ## Number of hits? ## 7189 ../output/02-Peve-lncRNA-align/lncRNA_lncRNA_blastn04.tab ## File header ## ::Porites_evermani_scaffold_1:422643-423512 ::Porites_evermani_scaffold_1:422643-423512 100.000 869 0 0 1 869 1 869 0.0 1568 ## ::Porites_evermani_scaffold_1:1084867-1089422 ::Porites_evermani_scaffold_1:1084867-1089422 100.000 4555 0 0 1 4555 1 4555 0.0 8215 ## ::Porites_evermani_scaffold_10:260427-263111 ::Porites_evermani_scaffold_10:260427-263111 100.000 2684 0 0 1 2684 1 2684 0.0 4841 ## ::Porites_evermani_scaffold_10:260427-263111 ::Porites_evermani_scaffold_10:260440-263111 100.000 2671 0 0 14 2684 1 2671 0.0 4818 ## ::Porites_evermani_scaffold_10:260440-263111 ::Porites_evermani_scaffold_10:260440-263111 100.000 2671 0 0 1 2671 1 2671 0.0 4818 ## ::Porites_evermani_scaffold_10:260440-263111 ::Porites_evermani_scaffold_10:260427-263111 100.000 2671 0 0 1 2671 14 2684 0.0 4818 ## ::Porites_evermani_scaffold_10:890033-892111 ::Porites_evermani_scaffold_10:890033-892111 100.000 2078 0 0 1 2078 1 2078 0.0 3748 ## ::Porites_evermani_scaffold_10:1071612-1085055 ::Porites_evermani_scaffold_10:1071612-1085055 100.000 13443 0 0 1 13443 1 13443 0.0 24243 ## ::Porites_evermani_scaffold_10:1071612-1085055 ::Porites_evermani_scaffold_10:1071808-1085055 100.000 13247 0 0 197 13443 1 13247 0.0 23890 ## ::Porites_evermani_scaffold_10:1071612-1085055 ::Porites_evermani_scaffold_10:1075979-1085055 100.000 9076 0 0 4368 13443 1 9076 0.0 16368