The SARS-CoV-2 genome alignment option
1
0
Entering edit mode
16 months ago
natasha.sernova ★ 3.9k

Dear all, Nowadays many scientists have to solve some problems related to SARS-CoV-2. The viral genomes are huge(~30kb). Is it correct, that to align several of them I have to put those fasta-genomes to a single file, add a reference genome to the same file and run a proper tool like MAFFT?

(like here - https://www.biostars.org/p/187360/) It will be my next question – what MAFFT-option I should use? Probably MAFFT-L-INS-i, since «More specifically, in Figure 1 in Le et al. [18], the advantage of MAFFT-L-INS-i (an iterative refinement method) over MAFFT-L-INS-1 (a progressive method) was clearly observed for a small number of sequences but not for thousands of sequences.» Thank you! Natalia Sernova

SARS-CoV-2 mafft MAFFT-L-INS-i • 584 views
ADD COMMENT
0
Entering edit mode

Unfortunately some genomes are elsewhere, I had to search other dbs to find most of them.

ADD REPLY
1
Entering edit mode

You could use the software/procedure nextstrain uses to build their alignments for SARS-CoV-2.

ADD REPLY
1
Entering edit mode
16 months ago
GenoMax 107k

Any particular reason you want to do this yourself? NCBI makes genome alignments easy to do via SARS-CoV-2 resource page. Select genomes you want and align. Even build a phylogenetic tree.

You could it all yourself by following plan you described as well.

ADD COMMENT

Login before adding your answer.

Traffic: 1572 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