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Re: Subroutine to parse BLAST

by erix (Vicar)
on Dec 06, 2010 at 18:04 UTC ( #875674=note: print w/ replies, xml ) Need Help??


in reply to Subroutine to parse BLAST

There are several versions and implementations of BLAST. Can we assume you use NCBI's blast+ : ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ?

There is a user_manual.pdf there, which specifies the possible output formats.

What output do you have to parse? Did you notice that BLAST can output in a table format (option -outfmt)? With that you can pipe the blast-produced alignment data straight into a database table, or, of course, into a perl program. BLAST+'s table-format makes parsing rather trivial.

Can you let us know which implementation and version of BLAST you use? Show the actual output? Nobody can guess what your output looks like... Maybe also tell us whether it's homework or not (because of the no-bioperl condition)?


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