Biostar Beta. Not for public use.
Clustering by sequence alignments
0
Entering edit mode
3.1 years ago
bbb • 60
Russian Federation

Which cluster method is better to use to cluster DNAs of different species based on alignment information (matches, deletions, insertion)? i.e. reference sequence - sequence of 4000 b.p. length, then feature set is 4000 * |{b.p. from reads which was matched exactly, b.p. insertions, deletions}| = 12000

ADD COMMENTlink
0
Entering edit mode

What about CD-HIT ??

ADD REPLYlink
0
Entering edit mode

CD-hit is very good to remove redundancy but is not adequate for clustering. I didn't understand the question asked, though. For clustering you need a metric of similarity or distance.

ADD REPLYlink
0
Entering edit mode

Starting with distance matrices, affinity propagation clustering has worked quite nicely for me.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1