Pred2ary BLAST options

Multiple sequence information for a protein can increase accuracy significantly. If you don't have multiple sequence data, you can obtain it using the BLAST search tool. You can read more about the tool on NCBI's web page: http://www.ncbi.nlm.nih.gov/BLAST/

Here are references for the methods accessed here:

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.

BLAST Options

The default options are used, along with the "NR" (non-redundant) database. If you want to use other options or databases, please run BLAST yourself, save the results to a file (HTML is OK, if you save a copy of the web page returned by the NCBI server), and load it in from the "load proteins" dialog.

Running BLAST locally

If you have the databases and programs installed on your machine, you can run the programs locally, rather than accessing NCBI's or another network server. Installing the programs is too complicated to explain here; see the NCBI web site for details.

For regular BLAST, Pred2ary runs blastall, and for PSI-BLAST, Pred2ary runs blastpgp. Please be sure the right program is in your path, and working (this involves setting up a ~/.ncbirc file on UNIX machines). Be sure they work with the NR database; i.e. a command like "blastall -p blastp -d nr -i some.seq" works.