HOMD User Documentation     
4-7] Full list of the BLAST Advanced options
BLASTN Program Advanced Options
-GCost to open a gap [Integer] NCBI default = 5; HOMD 16S rRNA search default = 5
-ECost to extend a gap [Integer] NCBI default = 2; HOMD 16S rRNA search default = 5
-qPenalty for a mismatch in the blast portion of run [Integer] NCBI default = -3; HOMD 16S rRNA search default= -5
-rReward for a match in the blast portion of run [Integer] NCBI default = 1; HOMD 16S rRNA search default = 4
-eExpectation value (E) [Real] default = 10.0
-WWord size, default is 11 for blastn, 3 for other programs.
-vNumber of one-line descriptions (V) [Integer] default = 100
-bNumber of alignments to show (B) [Integer] default = 100
-fThreshold for extending hits, default if zero blastp 11, blastn 0, blastx 12, tblastn 13 tblastx 13, megablast 0 [Integer] default = 0
-ZX dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 50, tblastx 0, all others 25 [Integer] default = 0
-yX dropoff value for ungapped extensions in bits (0.0 invokes default behavior) blastn 20, megablast 10, all others 7 [Real] default = 0.0
-SQuery strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] default = 3
-zEffective length of the database (use zero for the real size) [Real] default = 0
-KNumber of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer] default = 0
-P0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer] default = 0
-YEffective length of the search space (use zero for the real size) [Real] default = 0

BLASTP, BLASTX, TBLASTN Program Advanced Options
-GCost to open a gap [Integer] default = 11
-ECost to extend a gap [Integer] default = 1
-eExpectation value (E) [Real] default = 10.0
-WWord size, default is 11 for blastn, 3 for other programs.
-vNumber of one-line descriptions (V) [Integer] default = 100
-bNumber of alignments to show (B) [Integer] default = 100
-fThreshold for extending hits, default if zero blastp 11, blastn 0, blastx 12, tblastn 13 tblastx 13, megablast 0 [Integer] default = 0
-CUse composition-based statistics for tblastn: D or d: default (equivalent to F) 0 or F or f: no composition-based statistics 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001 2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally For programs other than tblastn, must either be absent or be D, F or 0. [String] default = D
-sCompute locally optimal Smith-Waterman alignments (This option is only available for gapped tblastn.) [T/F] default = F
-wFrame shift penalty (OOF algorithm for blastx) [Integer] default = 0
-ZX dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 50, tblastx 0, all others 25 [Integer] default = 0
-yX dropoff value for ungapped extensions in bits (0.0 invokes default behavior) blastn 20, megablast 10, all others 7 [Real] default = 0.0
-SQuery strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] default = 3
-zEffective length of the database (use zero for the real size) [Real] default = 0
-KNumber of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer] default = 0
-P0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer] default = 0
-YEffective length of the search space (use zero for the real size) [Real] default = 0 Limited values for gap existence and extension are supported for these three programs. Some supported and suggested values are: Existence Extension 10 1 10 2 11 1 8 2 9 2

Article last modified on 2014-04-08 11:01:02 by lyang; viewed 1489 times; Category: User Documentation; Topic: Tools & Downloa

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