Question: Alignment DNA sequence tool
gravatar for jaqy
5.1 years ago by
jaqy20 wrote:

Please can you give me a tool which return the score of alignment of all the 8-mer motifs between a DNA sequence (own sequence) and a set of sequences (22 500 sequences) ?
Thank you

alignment tools • 976 views
ADD COMMENTlink modified 5.1 years ago by Yongjie Zhang80 • written 5.1 years ago by jaqy20

Can you further explain exactly what you wish to accomplish?

ADD REPLYlink written 5.1 years ago by Brian Bushnell17k


thank you Brian Bushnell for your reply

I have a sequence of 1000 pb and I would like detect all the octamer pattern in this sequence and give a score for each detected pattern

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by jaqy20
gravatar for Yongjie Zhang
5.1 years ago by
UC Berkeley, USA/ Shanxi Univ, China
Yongjie Zhang80 wrote:

You may perform blast2 on the NCBI website with your own sequence as query and the 22500 sequences as subject although I'm not sure what's the max. number of subject sequences allowed. If that does not work, you may try local blast with the tabular output.

ADD COMMENTlink written 5.1 years ago by Yongjie Zhang80
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