MSA alignment library for Java
1
0
Entering edit mode
7.0 years ago
Bioaln ▴ 360
Hello. I've come across an alignment project, which requires me to 'implement simple MSA' in Java. I know there are many great tools out there, but as I am to implement my software I need a hint on how to align multiple fasta sequences and write that to an outfile for example. I can use any library or implement algorithm from the scratch. Workload is not going to be very intensive, so a basic algorithm might work. Are there any libraries meant to do that? If not, where can i find sources on how to implement my own msa? Thanks for help.
java sequence alignment • 2.4k views
ADD COMMENT
0
Entering edit mode
7.0 years ago
vassialk ▴ 200

If I correctly understand, look for Biojava or you can call BWA, Bowtie, BBMap, NextGene or use Ugene. Perhaps using Python or Ruby can be more laconic than Java.

ADD COMMENT
0
Entering edit mode

Thanks for reply. I just discovered some of there options include Java API, which will probably solve my problem. In the end I am aiming to have an jar without calling other software. Therefore calling other programs is not an option. Thanks

ADD REPLY

Login before adding your answer.

Traffic: 1692 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