July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 13: NCBI-BLAST Reference
-z [real number]
Default: 0
The effective length of a database; same as blastall.
-Z [integer]
Default: 50
The X dropoff value for a dynamic programming gapped extension.
bl2seq Parameters
bl2seq runs the basic BLAST searches on two sequences. Many parameters are identi-
cal between bl2seq and blastall, but some are unique to one program or the other,
and some parameters with the same symbol do different things.
Here are a few sample command lines:
bl2seq -p blastp -i protein1 -j protein2
bl2seq -p blastn -i nucleotide1 -j nucleotide2 -F F -D 1
bl2seq -p blastx -i nucleotide -j protein
bl2seq -p tblastn -i protein -j nucleotide
bl2seq -p tblastx -i nucleotide1 -j nucleotide2
The following reference describes the parameters for bl2seq.
-a [file]
Default: Optional
Specifies the SeqAnnot output file. The [file] will be in the Abstract Syntax Notation 1
(ASN.1) format for import into and use with the NCBI toolbox.
-A [T/F]
Default: F
Input sequences are NCBI identifiers. When set to T, the program makes an online connec-
tion to the NCBI databases to retrieve the FASTA sequences.
bl2seq -A -p blastx -i AF287139 -j AAG39070
(This function was just enabled in the 2.2.6 release.)
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