Good Poly-A Filtering Rules Or Tools

Question

[hbw]

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: SeqAnswers, StackExchange.

[Philipp Bayer]

The Poly A Sequences In Small Rna might be a good fit for you

[Biomonika (Noolean)]

Hi Philipp, after reading manual I could not find how to run Trimest for removing polyA from 5' prime (and just from 5'prime as it seems to expect to find polyT there)

[Biomonika (Noolean)]

I am also dealing with polyA tails and would be happy to learn more about the biology behind - when to expect them, in which amount..