blat - Standalone BLAT v. 36 fast sequence search command line tool

  blat database query [-ooc=11.ooc] output.psl
  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:
  With the second form, a sequence id of file:start-end will be used.
  -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.