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.
blat analysis
最新推荐文章于 2022-10-02 09:54:23 发布
Blat是一款由W.James Kent开发的快速比对工具,主要用于基因和ESTs的定位。它解决了BLAST的不足,如速度慢和处理结果复杂。Blat的特点是速度快,输出结果简洁,尤其适合小序列对大基因组的比对。它接受fasta格式输入,无需建库即可比对。Blat的输出结果为psl格式,包含详细比对信息。在使用时,需注意‘-t’和‘-q’参数类型一致,以及在不同类型的比对中如何正确设置参数。
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