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#2667: Use Mafft for nucleotide MSA #2667

Open GennadiyZakharov opened 5 months ago

GennadiyZakharov commented 5 months ago

Background

The JnJ team requested using Mafft for DNA/RNA sequence alignment.

Scope of work

Implement running MSA via Mafft
Add UI to choose alignment method (KAlign/Mafft) for macromolecules MSA.

Details

How to install Mafft

Bioconda: conda install bioconda::mafft
Binary deb package: wget https://mafft.cbrc.jp/alignment/software/mafft_7.520-1_amd64.deb
Source code: https://mafft.cbrc.jp/alignment/software/installation_without_root.html

Sample data

http://www.lbgi.fr/balibase/BalibaseDownload/BAliBASE_R10.tar.gz

Two sample files form this benchmark are attached to this ticket

Running Mafft

Fast run with default options mafft BBA0001.tfa > BBA0001.mafft.fasta

Slower run with iterative refinement mafft --genafpair --maxiterate 1000 BBA0001.tfa > BBA0001.mafft.E-INS-i.fasta

dnillovna commented 5 months ago

This issue has been mirrored in Jira: https://reddata.atlassian.net/browse/GROK-14906

dnillovna commented 1 month ago

This issue has been mirrored in Jira: https://reddata.atlassian.net/browse/GROK-16163