blast query using list instead of single .fa files from command line?
I have a large number of short sequences I want to blast against each other. is there a way (other than setting up a single pairwise query for each), to use two lists to get pairwise comparisons for hundreds of .fa files? Any help is appreciated.
• 703 views
•
link
written
by
goatsrunfaster •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to BLAST more than 5 sequences against UniProt database?
written by Riq •
-
integration using rPCA with reference or without it?
written by paria •
-
Comparing alignments of differing length - what's the right test?
written by ngarber •
-
How to deal with differences in sample size for metagenomic diversity based on abundance?
written by goatsrunfaster •
-
Use BLAST Command Line Applications to run a folder of many sequences against a database
written by daver.v •
-
Aligning to ultra-short reference sequence
written by spaladug •
-
Using 'blastn' to do a remote search on NCBI BLAST against the nt collection database
written by maciwuk •
-
How to perform BLAST search containing a large number of query sequences ?
written by siddharth.avadhanam •
-
Using Biopython for BLAST Queries is very slow
written by ncowen •
-
Get Pairwise Sequence Identity
written by Chris •
why don't you cat them in a single (big) file , created blast DB from it and then blast the file against the DB . Afterwards parse out all pairwise alignments.