Question

Redundancy Removal

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12.8 years ago

Matlab_Help_Plz ▴ 40

I've got a matrix of the percent ID of each of my sequences. What's a simple way with linear algebra to set a redundancy threshold. Like 95%.

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ADD COMMENT • link updated 12.7 years ago by scapella ▴ 390 • written 12.8 years ago by Matlab_Help_Plz ▴ 40

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What do you mean by "set a redundancy threshold"? It seems like the matrix you are describing is probably populated with a percentage, so I'm not sure what linear algebra has to do with things. Do you mean that you want a vectorized way of removing redundant sequences from some list?

ADD REPLY • link 12.8 years ago by Sean Davis 26k

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have you really got a matrix (AA) and not a vector (A1)?

ADD REPLY • link 12.8 years ago by Michael Schubert ★ 7.1k

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This question makes no sense, try again!

ADD REPLY • link 12.7 years ago by Michael 54k

score 0 · Answer 1 · 2011-08-08

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12.7 years ago

scapella ▴ 390

Hi, I don't know how to do it with "linear algebra" but you can still do it in a different way. For instance, you can use CD-Hit algorithm, the one used for reducing the NCBI Non-Redudant database redundancy, or if you have your sequences aligned, you could try a trimAl [http://trimal.cgenomics.org] where you set the redundancy threshold and the program applies a clustering algorithm for removing redundant sequences.