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Blast Screen

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 may be used for either completely rejecting sequences or for simply tagging the matching segments, or for both. If you wish to tag with several tag types, then several instances of the Blast screen module need to be used. 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: E value
This specifies the `E value' used by blast when determining which hits should be considered as real.
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. If you wish to accept everything, but still want to tag the matches, then set the match fraction to greater than 1.0.
Option: Tag type
The default for this is <none> which indicates no tagging is required. Otherwise this should be a 4 letter tag type (such as REPT) known to gap4.

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This page is maintained by staden-package. Last generated on 22 October 2002.