How To Cluster Sequences Based On Blast Results?
2
4
Entering edit mode
9.0 years ago
Cacau ▴ 500

I want to cluster a set of DNA sequences into families based on BLAST results. Is there any idea what software I can use to do it? Thanks!

clustering blast • 7.9k views
ADD COMMENT
1
Entering edit mode

What research into this question have you done already? A simple Google search for "blast cluster" returns several useful hits, for example http://www.biomedcentral.com/1471-2105/12/116.

ADD REPLY
0
Entering edit mode

Once again, your absolutely useless answer.

ADD REPLY
0
Entering edit mode

Seriously? This thread is 3.4 years old. Why do you think it's necessary to come and post this? It's always encouraged that users do some research on their own before asking questions.

Your reaction is not in line with the expected behavior/attitude of users on biostars so I would suggest you to rethink your statement.

ADD REPLY
0
Entering edit mode

There are many ways (and reasons) to cluster sequences, so try to provide more information about what you are doing. For starters, please indicate what you mean by "families" because it is not clear from your question. For example, do you mean some kind of taxonomic grouping above the species level (i.e. family-level clustering), or are you trying to identify gene families, or transposable element families, or something else? Is this data from a single species? And, is this a model species group you are studying? If you can provide some of those details, I'm sure you will get some helpful answers.

ADD REPLY
2
Entering edit mode
9.0 years ago
Digiomics ▴ 170

Maybe CLANS is what you are looking for. It clusters sequences based on an all-vs.-all blast search and gives you a nice visualization of the results, good to get first glimpse at the data.

ADD COMMENT
0
Entering edit mode

CLANS looks nice to me! Thanks so much!

ADD REPLY
2
Entering edit mode
9.0 years ago

Take also a look to MCL (and orthoMCL), and Silix.

ADD COMMENT
0
Entering edit mode

THX! These are very famous tools!

ADD REPLY

Login before adding your answer.

Traffic: 1433 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6