Author / Distributor
"The BLAST-Like Alignment Tool, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences" more details at BLAT
Also refer to Running Jobs on zcluster
last version is at /usr/local/blat/3.5 /usr/local/blat/latest always points to last version.
Example of a shell script sun.sh to run on at the batch queue:
#!/bin/bash cd working_directory time /usr/local/blat/latest/bin/blat [options]
Please contact us to statt gfServer before you run the project!
gfServer starting at zcluster:
gfServer start zcluster.rcc.uga.edu 17780 /db/blat/data/hg19.2bit & gfServer start zcluster.rcc.uga.edu 17783 /db/blat/data/hg18.2bit & gfServer start zcluster.rcc.uga.edu 17784 /db/blat/data/mm9.2bit & gfServer -trans -mask start zcluster.rcc.uga.edu 17785 /db/blat/data/hg18.2bit & gfServer -trans -mask start zcluster.rcc.uga.edu 17786 /db/blat/data/hg19.2bit & gfServer -trans -mask start zcluster.rcc.uga.edu 17787 /db/blat/data/mm9.2bit &
/usr/local/blat/latest/bin/blat blat - Standalone BLAT v. 35 fast sequence search command line tool usage: blat database query [-ooc=11.ooc] output.psl where: database and query are each either a .fa , .nib or .2bit file, or a list these files one file name per line. -ooc=11.ooc tells the program to load over-occurring 11-mers from and external file. This will increase the speed by a factor of 40 in many cases, but is not required output.psl is where to put the output. Subranges of nib and .2bit files may specified using the syntax: /path/file.nib:seqid:start-end or /path/file.2bit:seqid:start-end or /path/file.nib:start-end With the second form, a sequence id of file:start-end will be used. options: -t=type Database type. Type is one of: dna - DNA sequence prot - protein sequence dnax - DNA sequence translated in six frames to protein The default is dna -q=type Query type. Type is one of: dna - DNA sequence rna - RNA sequence prot - protein sequence dnax - DNA sequence translated in six frames to protein rnax - DNA sequence translated in three frames to protein The default is dna -prot Synonymous with -t=prot -q=prot -ooc=N.ooc Use overused tile file N.ooc. N should correspond to the tileSize -tileSize=N sets the size of match that triggers an alignment. Usually between 8 and 12 Default is 11 for DNA and 5 for protein. -stepSize=N spacing between tiles. Default is tileSize. -oneOff=N If set to 1 this allows one mismatch in tile and still triggers an alignments. Default is 0. -minMatch=N sets the number of tile matches. Usually set from 2 to 4 Default is 2 for nucleotide, 1 for protein. -minScore=N sets minimum score. This is the matches minus the mismatches minus some sort of gap penalty. Default is 30 -minIdentity=N Sets minimum sequence identity (in percent). Default is 90 for nucleotide searches, 25 for protein or translated protein searches. -maxGap=N sets the size of maximum gap between tiles in a clump. Usually set from 0 to 3. Default is 2. Only relevent for minMatch > 1. -noHead suppress .psl header (so it's just a tab-separated file) -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome. -repMatch=N sets the number of repetitions of a tile allowed before it is marked as overused. Typically this is 256 for tileSize 12, 1024 for tile size 11, 4096 for tile size 10. Default is 1024. Typically only comes into play with makeOoc. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate. -mask=type Mask out repeats. Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Types are lower - mask out lower cased sequence upper - mask out upper cased sequence out - mask according to database.out RepeatMasker .out file file.out - mask database according to RepeatMasker file.out -qMask=type Mask out repeats in query sequence. Similar to -mask above but for query rather than target sequence. -repeats=type Type is same as mask types above. Repeat bases will not be masked in any way, but matches in repeat areas will be reported separately from matches in other areas in the psl output. -minRepDivergence=NN - minimum percent divergence of repeats to allow them to be unmasked. Default is 15. Only relevant for masking using RepeatMasker .out files. -dots=N Output dot every N sequences to show program's progress -trimT Trim leading poly-T -noTrimA Don't trim trailing poly-A -trimHardA Remove poly-A tail from qSize as well as alignments in psl output -fastMap Run for fast DNA/DNA remapping - not allowing introns, requiring high %ID -out=type Controls output file format. Type is one of: psl - Default. Tab separated format, no sequence pslx - Tab separated format with sequence axt - blastz-associated axt format maf - multiz-associated maf format sim4 - similar to sim4 format wublast - similar to wublast format blast - similar to NCBI blast format blast8- NCBI blast tabular format blast9 - NCBI blast tabular format with comments -fine For high quality mRNAs look harder for small initial and terminal exons. Not recommended for ESTs -maxIntron=N Sets maximum intron size. Default is 750000 -extendThroughN - Allows extension of alignment through large blocks of N's
Source code downloaded from BLAT