BLAST

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Chapter 13: NCBI-BLAST Reference

-W [1..3]

Default: 3

The word size; same as blastall.

-X [integer]

Default: 15

The X dropoff for gapped alignments; same as blastall.

-y [real number]

Default: 7.0

X dropoff for ungapped extensions; same as blastall

-Y [real number]

Default: 0

The effective length of the search space; same as blastall.

-z [real number]

Default: 0

The effective database size; same as blastall.

-Z [integer]

Default: 25

The X dropoff for final gapped alignment; same as blastall.

blastclust Parameters

blastclust clusters a database of protein or nucleotide sequences. It outputs rows of

sequence identifiers from the database with clustered sequences occurring on the

same row and clusters sorted from largest to smallest. The program can generate a

list of clusters for input into another program (e.g., an alignment program such as

PHRAP); however, it should be used only on a relatively small number of sequences

(10-1000) because it runs only on a single computer, and the RAM requirements

quickly exceed most capacities.

Here are a few sample command lines:

blastclust -i my_nucdb -p F -o my_nucdb.clusters

blastclust -i my_pepdb -o my_pepdb.clusters -L 0.7 -S 90

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