Pseudocode for gapped BLAST seed extension

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3.5 years ago

Daniel ▴ 10

Hello all,

I am trying to understand in detail how does the gapped BLAST seed extension DP algorithm works. Despite searching for days now, I could not find anywhere a pseudocode that would allow implementing this in python. Not being a C programmer, it would be impossible for me to grasp this from the BLAST source code.

Can anyone help me with this?

Thank you all. Best,

Daniel

Pseudocode smith-waterman seed extend BLAST • 963 views

ADD COMMENT • link updated 3.5 years ago by GenoMax 148k • written 3.5 years ago by Daniel ▴ 10

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Did you check the (original) manuscript on the blast algorithm(s) ?

With a bit of searching you should be able to get them from the NCBI website

ADD REPLY • link 3.5 years ago by lieven.sterck 15k

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Hi lieven.sterck, thanks for your reply. The original article is the first place where I checked. Trust me, I looked on every single online resource (from university lectures, to papers). No one provides a pseudocode describing how the gapped seed extension works. Daniel

ADD REPLY • link 3.5 years ago by Daniel ▴ 10

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