Question: Equivalent Blast And Blast+ Commands
3
gravatar for Marina Manrique
9.2 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

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

blast • 5.5k views
ADD COMMENTlink modified 6.3 years ago by Adam R20 • written 9.2 years ago by Marina Manrique1.3k
3
gravatar for Casey Bergman
9.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

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

ADD COMMENTlink modified 12 months ago by RamRS30k • written 9.2 years ago by Casey Bergman18k
3
gravatar for Michael Dondrup
9.2 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

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)

ADD COMMENTlink modified 12 months ago by RamRS30k • written 9.2 years ago by Michael Dondrup47k
0
gravatar for Adam R
6.3 years ago by
Adam R20
United States
Adam R20 wrote:

There's a nice diagram in the manual


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

ADD COMMENTlink written 6.3 years ago by Adam R20
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