Equivalent Blast And Blast+ Commands

Question

[Marina Manrique]

Hi all,

I used to use an old blast version (2.2.21) and now I'm moving to the latest blast+ version (2.2.25).

The thing is I don't know which options in the 2.2.25 version are the options equivalent to -F and -I options in the 2.2.21 one.

Anyone knows? and anyone knows where I could get the manual for the blast 2.2.21 or a similar version?

Thanks!

Marina

Answer 1

[Casey Bergman]

From: http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.3_Quick_start

The easiest way to get started using these command line applications is by means of the legacy_blast.pl PERL script which is bundled along with the BLAST+ applications. To utilize this script, simply prefix it to the invocation of the C toolkit BLAST command line application and append the --path option pointing to the installation directory of the BLAST+ applications. For example, instead of using blastall -i query -d nr -o blast.out, use legacy_blast.pl blastall -i query -d nr -o blast.out --path /opt/blast/bin

Answer 2

[Michael]

Blast: -F -F Filter query sequence (DUST with blastn, SEG with others) [String]

Blast+: -dust: Arguments to DUST filtering algorithm (use ‘no’ to disable).

Blast: -l Restrict search of database to list of GI's [String] Optional

Blast+: -gilist: File containing a list of GIs to restrict the BLAST database to search. The expect values in the BLAST results are based upon the sequences actually searched and not on the underlying database.

ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blastall.html (Blast)

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.24/user_manual.pdf (Blast+, there is no user_manual.pdf in the LATEST folder)

Answer 3

[Adam R]

There's a nice diagram in the manual

http://www.ncbi.nlm.nih.gov/books/NBK1763/#_CmdLineAppsManual_Appendix_A_Conversion_