note - FIZ Karlsruhe

Advanced similarity searching
Changing BLAST parameters
To change a setting, a parameter code must be appended to the basic RUN BLAST command.
The single-letter code must be prefixed with a hyphen, followed by a space and a valid value. The
complete list of BLAST advanced options and acceptable values is given on page 137.
Example: protein BLAST with the low complexity filter turned off
=> RUN BLAST L1 /SQP –F F
Example: protein BLAST using the PAM-30 matrix
=> RUN BLAST L1 /SQP -M PAM30
A series of codes and values can be combined together into a single online command.
Example: using word size of 2, filter turned off (F), e-Value of 20,000, and the PAM-30 matrix
=> RUN BLAST GSSFLSPEHQR /SQP –W 2 –F F –E 20000 –M PAM30
note
Helpful
HINT
When altering any BLAST settings specifying the search type (/SQN, /SQP
or /TSQN) is absolutely necessary. As the parameters valid for each search
type are different, this must be clearly stated. RUN BLAST will not accept
any parameters if the type of sequence search is not specified.
The National Center of Biotechnology Information (NCBI) provides detailed
user documentation on the BLAST algorithm, the basics of similarity searching
using BLAST, and the effective use of advanced BLAST parameters.
BLAST tutorials:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
NCBI handbook:
http://www.ncbi.nlm.nih.gov/books/NBK21097/
Page 50 | GENESEQ on STN (DGENE) Workshop Manual