Differences

This shows you the differences between two versions of the page.

--- blast_protocol [2021/09/12 15:20] – 38.20.199.40
+++ blast_protocol [2022/09/06 14:49] (current) – 134.190.232.106
@@ Line 6: / Line 6: @@
   - __tblastn__: search translated nucleotide database with protein sequence query
   - __tblastx__: search translated nucleotide database with translated nucleotide sequence query
+{{:blast.png?400|}}
 //**blastp** can usually provide better hit alignments than blastn, especially for distantly related species.This is partially because amino acids sequences are more conserved than nucleotides (Koonin and Galperin, 2002).//
@@ Line 86: / Line 88: @@
     > python blastxml_to_tabular.py -o output.tabular -c qseqid,qlen,salltitles,sseqid,slen,bitscore,qframe,pident,evalue,qstart,qend,sstart,send,length input.xml
 </code>
+#This is another way to parse BLAST outputs via using -outfmt '6 qseqid sseqid ...'
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -pe threaded 2
+#$ -cwd
+source activate blast
+export BLASTDB= /misc/scratch3/rogerlab_databases/other_dbs/nr_010621
+DB=nr
+query=ATCG00670.1.fasta
+blastp -db $DB -query $query -out /scratch2/xizhang/BLASTP_nr.tsv -num_threads 2 -outfmt '6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle'
+source deactivate
+</code>
+Sep 6th,2022 Since Diamond is faster on BLASTP and BLASTx, this is another way using Diamond
+<code>
+#!/bin/bash
+#$ -S /bin/bash
+. /etc/profile
+#$ -pe threaded 40
+#$ -cwd
+source activate /scratch2/software/anaconda/envs/diamond-2.0.7
+#DB=nr
+while read line
+do
+diamond blastp -p 40 -k 5 -e 1e-10 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle salltitles --header -d /misc/scratch3/rogerlab_databases/other_dbs/nr_02032022/diamond_nr.dmnd -q $line -o BLASTP_nr.$line.tsv --sensitive
+done <$1
+conda deactivate
+</code>
 **V5 NCBI database**