Output blastx top hits as fasta of the original sequences
I have performed a blastx of 1,000,000,000 short sequences against a small database. This took a while,
blastall -p blastx -i infile.fa -d prot_blastdb -o outfile.txt -m 8 -S 3 -b 1 -e 0.001
I then filtered the original fasta file to pull out those with top hits. I can share my awk script for this if asked, but i'm wondering if there is a way to get blast to output the fasta sequences directly to a file as it finds them. It seems silly making two passes of the same file.
• 2,279 views
•
link
written
by
bonsalldavid •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Blastx issue
written by Avik •
-
How can I extract upstream regions in fasta for all blastx hits locally performed on nr database?
written by mrj •
-
Puzzling NCBI BLAST+ output after transcriptome assembly
written by ella •
-
Can't grep qseqid (column 1) from blastx outfmt6
written by ladypurrsia •
-
ncbi blast results in multi-sequence fasta file
written by a.rex
-
BLAST options error: tried to set option (130) and value (1), line (537)
written by oliver.bayfield •
-
phylogeny tree after a blastx run
written by arronar
-
How To Blast A Fasta File That Is Non-16S
written by pfryling •
-
Blastall Vs Blast+ Problem With Filter Dust
written by adam.skowron •
-
Getting Top 10 Sequences Of Blast Results Bio Python
written by Ankur •
...just had a thought. There might be faster options for filtering (eg hashing??) if blast output a numerical index for each read. I could add this artificially by prefixing the read name, but this would be a last resort I think.
Use
blastdbcmdutility (part of blast+) along with a list of accession numbers (one per line in a file with -entry_batch option with blastdbcmd) you are interested in to retrieve the sequences you need. While this is still a two step process it is reasonably fast.