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Blast Screen

Filename
blast.p4m

Description
This module uses the blastall program to compare all the input sequences against a prebuilt blast database of screen sequences. It is not possible to compare against a subset of the database - to do this build a new blast database using formatdb. This module is an alternative to the Screen Sequences module which uses the screen_seq program. Blast is not included as part of the Staden Package. It is available from the NCBI.

Option: BLAST database
This is the filename of the BLAST database to screen against, with the `.nhr', `.nin' and `.nsq' suffixes removed.

Option: Match fraction
This is the total percentage of the sequence which much have a blast match somewhere in the BLAST database searched in order to reject this sequence. Segments of the input sequence that match multiple components in the BLAST database are only counted once when computing this percentage, but the locations of the matches in the BLAST database do not need to be consecutive.

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_21.html