Entering edit mode
3.8 years ago
Nicolas Carter
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10
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.
I don't think needle is up for the task. Try minimap2 or mummer
What format is your data in, fasta? You would need an aligner like LASTZ in addition to the two options mentioned by @Asaf.