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Seed And Extend Algorithm

Can anyone recommend any good reviews on seed and extend alignment algorithms? (Or sequence alignment algorithm in general)

thanks!

alignment
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updated by scapella scapella • written by Bioscientist Bioscientist

3 answers

Start by reading this review (A survey of sequence alignment algorithms for next-generation sequencing). Then go over the references and select the paper for the tool you are more interested on.

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written by Drio Drio

The author of LASTZ (Bob Harris) has a thesis here(pdf) that I think is pretty comprehensive and readable.

It covers seeds, spaced seeds, gapped and gap-free extension, "quantum sequences" and others.

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written by brentp brentp

Hi,

If you are looking for a nice review in Multiple Sequence Alignment programs/algorithms, I'd like to recommend you this one http://www.ncbi.nlm.nih.gov/pubmed/19648142. It was written a couple of years ago for one of the most active guy in the field. I hope that helps you.

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written by scapella scapella

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