blat analysis

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:

   库序列        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:

  查询序列       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.