<![CDATA[BOL: BLAST options, setting and defaults]]> https://bioinformaticsonline.com/bookmarks/view/38389/blast-options-setting-and-defaults? https://bioinformaticsonline.com/bookmarks/view/38389/blast-options-setting-and-defaults Mon, 10 Dec 2018 08:29:37 -0600 https://bioinformaticsonline.com/bookmarks/view/38389/blast-options-setting-and-defaults <![CDATA[BLAST options, setting and defaults]]> BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.

A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

 BLASTNBLASTPBLASTXTBLASTNTBLASTXPSIBLAST
Gap opening penalty:
cost to open a gap [integer]		 default = 5 default = 11
limited values are supported		 default = 11
limited values are supported		 default = 11
limited values are supported		 default = 11
limited values are supported		 default = 5
Gap extension penalty:
cost to extend a gap [integer]		 default = 2 default = 1
a 0 in this field means to use the default		 default = 1
a 0 in this field means to use the default		 default = 1
a 0 in this field means to use the default		 default = 1
a 0 in this field means to use the default		 default = 2
Nucleic match:
reward for a match in the BLAST portion of run [integer]		 default = 1 n/a n/a n/a n/a default = 1
Nucleic mismatch:
penalty for a mismatch in the blast portion of run [integer]		 default = -3 n/a n/a n/a n/a default = -3
Expectation value:
(E) [real]		 default = 10.0 default = 10.0 default = 10.0 default = 10.0 default = 10.0 default = 10.0
Word size:
the size of the initial word that must be matched between the database and the query sequence		 default = 11 default = 3 default = 3 default = 3 default = 3 default = 11
Max scores:
Number of one-line descriptions (V) [Integer]		 default = 25 default = 25 default = 25 default = 25 default = 25 default = 25
Max alignments:
number of alignments to show (B) [integer]		 default = 15 default = 15 default = 15 default = 15 default = 15 default = 15
Query filter:
filter applied to the query sequence		 default = DUST default = SEG default = SEG default = SEG default = SEG default = DUST
Query genetic code:
genetic code to be used in BLASTX translation of the query		 n/a n/a default = universal default = universal default = universal n/a
Matrix:
substitution matrix to be used for amino acid comparisons		 no default default = blosum62 default = blosum62 default = blosum62 default = blosum62 no default

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps OpenGap Extension
10 1
10 2
11 1
8 2
9 2

Address of the bookmark: https://www.arabidopsis.org/Blast/BLASToptions.jsp

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