Question: Aligning two genomes
gravatar for Nicolas Carter
2 days ago by
Nicolas Carter10 wrote:

Hello everyone, I'm trying to align two sequences with EMBOSS needle (global alignment). Specifically, they are the genomes of Sars-CoV-2, but one of the sequences (MT259240) doesn't have certain regions (the non-coding regions like 5'UTR and 3'UTR), so, I suspect that the alignment may be not quite right. Namely, the first non-coding region of the first sequence (NC_045512 the referent sequence) is being aligned with the first gene of the other sequence (ORF1ab gene). Is this incorrect and if so how would I correct the mistake? Thanks in advance.

alignment genome • 58 views
ADD COMMENTlink written 2 days ago by Nicolas Carter10

I don't think needle is up for the task. Try minimap2 or mummer

ADD REPLYlink written 2 days ago by Asaf8.0k

What format is your data in, fasta? You would need an aligner like LASTZ in addition to the two options mentioned by @Asaf.

ADD REPLYlink written 2 days ago by genomax85k
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