#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: 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.
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.
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
## 7018ls ../../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.ntohttps://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fa
cd ../data/
curl -O https://gannet.fish.washington.edu/seashell/snaps/Porites_evermanni_v1.fahead ../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_genomels ../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.ntohttps://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.fahead ../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_proteomels ../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.ptols ../../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???
/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 6echo "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/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/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../../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 6Note
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 6Note
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 6Note
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