Changes to Stanford BLAST server defaults

[Mike Cherry]

The Yeast and Arabidopsis specific BLAST WWW server has been modified
to use the "dust" filter by default for nucleic acid query
sequences. The dust filter masks out simple repeat and high AT rich
regions from the query sequence. The resulting sequences contains Ns
at the masked positions. This masking or filtering allows the search
to go faster and generally reports more interesting hits. With all the
simple repeats removed you can more easily see hits of the unique
regions of your sequence. If however you wish to turn the filtering
off just select "none" from the Filter Options menu on the BLAST form.

>From the beginning of the SGD and AtDB BLAST servers all peptide query
sequences have by default had the "seg" filter applied to them. The
seg filter removes simple repeats in a manner specific for peptide
sequences.

Mike

J. Michael Cherry                   Internet: cherry at genome.stanford.edu
Department of Genetics              Stanford University School of Medicine
Medical Center, Room A351           Stanford, California  94305-5120
Voice: 650-723-7541                 FAX: 650-723-7016

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            e-mail:    yeast-curator at genome.stanford.edu
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