Reliable alignment tool for similar sequences of similar length other than Mummer?
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5.1 years ago
nchuang ▴ 260

Still new to all this, but I am looking at a collection of similar sequences that are of the same length. I had been using Mummer to align the sequences to a reference. Unfortunately I have been doing it in a cumbersome way by extracting the aligned sequence with Bioperl based on the coord file from Mummer. I did not realize that by doing it this way I am not accounting for large deletions and possibly insertions (meaning my extracted sequences has no gaps when there should be).

My understanding is I should be looking for global alignment but with these indels would I want glocal alignment? What would be best for this if Mummer cannot do this? I feel mummer's algorithm would be perfect for glocal alignment but I don't know how to make it just give me a fasta file as oppose to delta/coord files.

Also I have been testing MAFFT and Tcoffee for this and they work well as far as I can tell. I am just wondering if that is overkill since they are Multiple sequence aligners.

alignment Mummer • 1.6k views
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Take a look at LASTZ. You may want to look at the link that says (newer versions, unreleased).

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Note that at least one option to get the sequence outputted is to use the delta2maf program. The program is not part of mummer but I uploaded it here https://github.com/cmdcolin/whole_genome_alignment_pipeline/tree/master/util

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3.9 years ago
novice ★ 1.0k

From what I understand, you're looking for an aligner optimized for split-alignment. If that is the case, then standard BWA-SW does that. I would also recommend YAHA, which I found more sensitive than BWA. Both of these support relatively large queries.

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