trimest

trimest

---

trimest trims poly-A tails off EST sequences.

Here is a sample session with trimest:

% trimest embl:hsfau hsfau.seq

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outseq] (seqoutall)

Output sequence(s) USA.

Optional qualifiers:

-minlength (integer)

This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. If there are mismatches in the tail, there must be at least this length of poly-A tail before the mismatch for the mismatch in order to be considered as part of the tail.

-mismatches (integer)

If there are this number or fewer contiguous non-A bases in a poly-A tail and there are -minlength A bases before them, they are considered part of the tail and removed. For example, the terminal 4 A's of GCAGAAAA would be removed with the default values of -minlength=4 and -mismatches=1 (There are not at least 4 A's before the last "G," so only the A's after it are considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; there are at least -minlength A's preceeding the last "G", so it is part of the tail.

-[no]reverse (boolean)

When a poly-T region at the 5' end of the sequence is found and removed, it is likely that the sequence is in the reverse sense. This option will change the sequence to the forward sense when it is written out. If this option is not set, the sense will not be changed.

Advanced qualifiers:

-[no]fiveprime (boolean)

If this is set true, the 5' end of the sequence is inspected for poly-T tails. These are removed if they are longer than any 3' poly-A tails. If this is false, the 5' end is ignored.