Question

Redundancy Removal

0

Entering edit mode

13.4 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%.

similarity • 2.4k views

ADD COMMENT • link updated 13.3 years ago by scapella ▴ 390 • written 13.4 years ago by Matlab_Help_Plz ▴ 40

3

Entering edit mode

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 13.4 years ago by Sean Davis 27k

0

Entering edit mode

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

ADD REPLY • link 13.4 years ago by Michael Schubert ★ 7.1k

0

Entering edit mode

This question makes no sense, try again!

ADD REPLY • link 13.3 years ago by Michael 55k

score 0 · Answer 1 · 2011-08-08

0

Entering edit mode

13.3 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.