Blastpgp manual

blastpgp, megablast, rpsblast) Use words of size N (length of best perfect match; zero invokes default behavior, except with megablast, which defaults to 28, and blastpgp, which defaults to 3. The default values for the other commands vary with "program": 11 for . This manual page documents briefly the commands bl2seq, blast, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, and seedtop. These commands are documented together because they have a lot of common options. blastpgp performs gapped blastp searches and can be used to perform iterative searches in psi-blast and phi-blast mode. Blastpgp (NCBI's implementation of PSIBLAST) was written for NCBI by Tom Madden and Alejandro Schaffer. Eric Cabot developed the PSIBLAST client by extensively modifying the BLAST client written by Ted Slater for Version of the Wisconsin Package.

Default value is: blastpgp. Pattern File Upload. Pattern file for PHI-BLAST functionality. This file needs to be in the style of a prosite entry file, with at least an ID line, PA line and optional HI line. Step 4 - Submission Job title. It's possible to identify the tool result by giving it a name. The three functions for calling the “legacy” NCBI BLAST command line tools blastall, blastpgp and rpsblast were declared obsolete in Biopython Release , deprecated in Release , and removed in Release Please use the BLAST+ wrappers in www.doorway.ruations instead. blastpgp must be executed with -C option followed by a file name to save position specific score matrix. blastall with "-p psitblastn" option executes PSI-TBLASTSN search, and -R option followed by a file name specifying the file that contains position specific score matrix.

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