Commit 3fbcda43 authored by peguerin's avatar peguerin
Browse files

revision blast uniprot

parent 3a492626
......@@ -13,7 +13,13 @@ awk '!/#/' diplodus/diplodus_CDS_nonsynonymous.vcf | wc -l
## seek known uniprot reference on the genome flanking sequence of non synonymous SNPs
#### get flanking region of non synonymous SNPs
i="diplodus"
i="mullus"
anvage flank -f ${i}_CDS_nonsynonymous.vcf -g genomes/${i}_genome_lgt6000.fasta -w 200 -o ${i}_CDS_nonsynonymous;
#### blast flanking sequences against uniprot
blastx -db swissprot_nucl -query "diplodus_CDS_nonsynonymous_flanking.fasta" -task blastx -outfmt "7 delim=, qacc sacc evalue bitscore qcovus pident" -max_target_seqs 5 > diplodus_CDS_nonsynonymous_uniprot.blastout
\ No newline at end of file
###### diplodus
blastx -db swissprot_nucl -query "diplodus_CDS_nonsynonymous_flanking.fasta" -task blastx -outfmt "7 delim=, qacc sacc evalue bitscore qcovus pident" -max_target_seqs 5 > diplodus_CDS_nonsynonymous_uniprot.blastout
bash blastout2tsv.sh diplodus_CDS_nonsynonymous_uniprot.blastout diplodus_CDS_nonsynonymous
###### mullus
blastx -db swissprot_nucl -query "mullus_CDS_nonsynonymous_flanking.fasta" -task blastx -outfmt "7 delim=, qacc sacc evalue bitscore qcovus pident" -max_target_seqs 5 > mullus_CDS_nonsynonymous_uniprot.blastout
bash blastout2tsv.sh mullus_CDS_nonsynonymous_uniprot.blastout mullus_CDS_nonsynonymous
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