Good Morning Peng:
You can search for short sequences, exact match, from 5 to 16 characters
in length with the kent source tree program: findMotif
in src/utils/findMotif/
--Hiram
Peng Yu wrote:
> Blat has a lower limit of the sequence that can searched (20bp). But I
> do want to search a short sequence in a very limited genomic region
> say chr1:xxxxxxx-yyyyyy. I'm wondering if there is an easy way to do
> so.
findMotif - find specified motif in sequence
usage:
findMotif [options] -motif=<acgt...> sequence
where:
sequence is a .fa , .nib or .2bit file or a file which is a list of
sequence files.
options:
-motif=<acgt...> - search for this specified motif (case ignored, [acgt]
only)
-chr=<chrN> - process only this one chrN from the sequence
-strand=<+|-> - limit to only one strand. Default is both.
-bedOutput - output bed format (this is the default)
-wigOutput - output wiggle data format instead of bed file
-verbose=N - set information level [1-4]
NOTE: motif must be longer than 4 characters, less than 17
-verbose=4 - will display gaps as bed file data lines to stderr
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