Question

Seed And Extend Algorithm

3

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12.7 years ago

Bioscientist ★ 1.7k

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

thanks!

alignment • 11k views

ADD COMMENT • link updated 12.7 years ago by scapella ▴ 390 • written 12.7 years ago by Bioscientist ★ 1.7k

score 5 · Answer 1 · 2011-08-03

5

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12.7 years ago

Drio ▴ 920

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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score 2 · Answer 2 · 2011-08-03

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12.7 years ago

brentp 24k

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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score 0 · Answer 3 · 2011-08-09

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12.7 years ago

scapella ▴ 390

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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