Blat

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Category

Bioinformatics

Program On

zcluster

Version

3.5

Author / Distributor

Jim Kent, UCSC

Description

"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

Running Program

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 &

Documentation

BLAT Program Specifications, Web

 
/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

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Installation

Source code downloaded from BLAT

System

64-bit Linux