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I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have mismatches/errors. What is a good rule or available tools that will handle the usual cases?

A few examples of the non-trivial cases I found, with their Genbank Accs:

>EE409337
... AAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTGTC
>EE409340
... TTTCTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTGTC
>EE409361
... TTGTTAAACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCATGTCGGC
TTACTGAATTGAA
>EE420306
.... AAAAAAAGTTATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAAAAAA
AAAAAAAAAAAAAAAAA

Cross-posted on SeqAnswers,Biostars.

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Did the answer on Biostars not work for you? (If so, what is it that it doesn't do that you would like it to do?) –  dd3 Jul 10 '13 at 20:22
    
@dd3: trimest has an option for trimming the poly-A regions, but we have to specify the rules. I have already done the basic filtering, but what are the "good" rules? Is there something better than min-length and max-mismatches that will handle real sequences I have given examples of? –  highBandWidth Jul 10 '13 at 20:34
1  
You could try the empirical approach. Take a random sample of N ESTs and calculate the distributions for min-length and max-mismatches. Use the distributions to pick appropriate cutoffs (some sort of statistics thing). –  dd3 Jul 10 '13 at 20:55
    
@dd3, that definitely makes sense and seems like a good idea. (although there's some judgement to be made for things like ...GAGAACTGGGCAAAA: where does the tail start?). Since EST processing is well established, shouldn't something like this already exist in the tools or the literature? How does everyone else do it? –  highBandWidth Jul 11 '13 at 3:09
    
I'm still a little unclear as to what you are trying to achieve that min length was failing (as you seem to be fine with trimming. Are you wanting to trim from ACA... on 409340 and AAACTGA... on 409361 but don't want to set min-length less than 7? –  Atl LED Jul 11 '13 at 3:13

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