blat - Standalone BLAT v. 36 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 of these files with one file name per line.
-ooc=11.ooc tells the program to load over-occurring 11-mers from
an external file. This will increase the speed
by a factor of 40 in many cases, but is not required.
output.psl is the name of the output file.
Subranges of .nib and .2bit files may be 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 alignment. 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 relevant for minMatch > 1.
-noHead Suppresses .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 comes into play only 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. Query sizes must not exceed 5000.
-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 Ns.