This directory contains the Blat application for stand-alone use.
Please note that the Blat source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
For help installing and running Blat please see:
- Documentation: http://genome.ucsc.edu/goldenPath/help/blatSpec.html
- FAQs: http://genome.ucsc.edu/FAQ/FAQblat.html
Name Last modified Size Description
Parent Directory -
FOOTER.txt 2016-11-02 07:59 11K
gfServer 2024-10-15 20:10 5.6M
gfPcr 2024-11-06 13:08 5.9M
isPcr 2024-11-06 13:08 6.0M
gfClient 2024-11-06 13:08 6.2M
blat 2024-11-06 13:08 6.3M
================================================================
======== blat ====================================
================================================================
blat - Standalone BLAT v. 36x2 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 relevent 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.
================================================================
======== gfClient ====================================
================================================================
gfClient v. 36x2 - A client for the genomic finding program that produces a .psl file
usage:
gfClient host port seqDir in.fa out.psl
where
host is the name of the machine running the gfServer
port is the same port that you started the gfServer with
seqDir is the path of the .nib or .2bit files relative to the current dir
(note these are needed by the client as well as the server)
in.fa is a fasta format file. May contain multiple records
out.psl is where to put the output
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
-prot Synonymous with -t=prot -q=prot.
-dots=N Output a dot every N query sequences.
-nohead Suppresses 5-line psl header.
-minScore=N Sets minimum score. This is twice 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.
-out=type Controls output file format. Type is one of:
psl - Default. Tab-separated format without actual 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
-maxIntron=N Sets maximum intron size. Default is 750000.
================================================================
======== gfServer ====================================
================================================================
gfServer v 36x2 - Make a server to quickly find where DNA occurs in genome
To set up a server:
gfServer start host port file(s)
where the files are .nib or .2bit format files specified relative to the current directory
To remove a server:
gfServer stop host port
To query a server with DNA sequence:
gfServer query host port probe.fa
To query a server with protein sequence:
gfServer protQuery host port probe.fa
To query a server with translated DNA sequence:
gfServer transQuery host port probe.fa
To query server with PCR primers:
gfServer pcr host port fPrimer rPrimer maxDistance
To process one probe fa file against a .nib format genome (not starting server):
gfServer direct probe.fa file(s).nib
To test PCR without starting server:
gfServer pcrDirect fPrimer rPrimer file(s).nib
To figure out usage level:
gfServer status host port
To get input file list:
gfServer files host port
options:
-tileSize=N Size of n-mers to index. Default is 11 for nucleotides, 4 for
proteins (or translated nucleotides).
-stepSize=N Spacing between tiles. Default is tileSize.
-minMatch=N Number of n-mer matches that trigger detailed alignment.
Default is 2 for nucleotides, 3 for proteins.
-maxGap=N Number of insertions or deletions allowed between n-mers.
Default is 2 for nucleotides, 0 for proteins.
-trans Translate database to protein in 6 frames. Note: it is best
to run this on RepeatMasked data in this case.
-log=logFile Keep a log file that records server requests.
-seqLog Include sequences in log file (not logged with -syslog).
-ipLog Include user's IP in log file (not logged with -syslog).
-syslog Log to syslog.
-logFacility=facility Log to the specified syslog facility - default local0.
-mask Use masking from nib file.
-repMatch=N Number of occurrences of a tile (n-mer) that triggers repeat masking the
tile. Default is 1024.
-maxDnaHits=N Maximum number of hits for a DNA query that are sent from the server.
Default is 100.
-maxTransHits=N Maximum number of hits for a translated query that are sent from the server.
Default is 200.
-maxNtSize=N Maximum size of untranslated DNA query sequence.
Default is 40000.
-maxAaSize=N Maximum size of protein or translated DNA queries.
Default is 8000.
-canStop If set, a quit message will actually take down the server.
================================================================