Fast all to all global alignment
1
3
Entering edit mode
5.0 years ago
Dray ▴ 30

I need to perform a global all to all sequence alignment of 10k sequences (this needs to be done for many datasets, sequence lengths 150-300aa). Currently the fastest way I could find is to use emboss needleall, however it still takes >10 hours per dataset. Would be great if anyone would share a faster solution!

alignment • 840 views
ADD COMMENT
0
Entering edit mode

Clustal-Omega or T-Coffee =) 10 years ago they were great...

ADD REPLY
0
Entering edit mode

USEARCH: https://drive5.com/usearch/manual/cmd_allpairs_global.html

VSEARCH: https://github.com/torognes/vsearch

Sorry, wrote this comment before but removed it unintentionally

ADD REPLY
0
Entering edit mode
5.0 years ago
lagartija ▴ 160

What kind of alignment ? What for ? The first software I would suggest is diamond

ADD COMMENT

Login before adding your answer.

Traffic: 1176 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