Question: match, mismatch, gap parameters for short DNA motifs
gravatar for odoluca
22 months ago by
Turkey/Izmir/Izmir University of Economics
odoluca20 wrote:

Hello all,

I have millions of short DNA sequences (20-150 nt) and I suspect some of these show similarity. I would like to compare them using pairwise alignment method, however, I am having trouble in determining which match score, mismatch penalty and gap penalty (linear method) I should use. My research didnt result any guideline for such short sequences, so any help is appreciated.

dna pairwise alignment motif • 794 views
ADD COMMENTlink written 22 months ago by odoluca20

Are these in fasta format? You may want to use CD-HIT to reduce redundancy instead of trying to do pair-wise alignments.

ADD REPLYlink written 22 months ago by genomax76k

I checked the CD-HIT. Its webservers don't allow any file bigger than 50 MBs. So I have to compile myself. However, I already coded a pairwise comparison algorithm, so I want to stick with it, in which otherwise would take longer. Thanks anyways.

ADD REPLYlink written 22 months ago by odoluca20
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