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TRIMEST application details page
Trim poly-A tails off EST sequences
EST and mRNA sequences often have poly-A tails at the end of them. Thisutility removes those poly-A tails. EST sequences are often the reverse complement of the correspondingmRNA's forward sense and have poly-T tails at their 5' end. By default,this program also detects and removes these and writes out the reversecomplement of the sequence. trimest is not infallible. There are often repeats of 'A' (or'T') in a sequence that just happen by chance to occur at the 3' (or 5')end of the EST sequence. trimest has no way of determining if theA's it finds are part of a real poly-A tail or are a part of thetranscribed genomic sequence. It removes any apparent poly-A tails thatmatch its criteria for a poly-A tail. trimest looks for a repeat of at least '-minlength' A's at the 3'end (and, by default, '-minlength' T's at the 5' end). If there are anapparent 5' poly-T tail and a poly-A tail, then it removes whichever isthe longer of the two. By default, it will allow '-mismatches' non-A (or non-T) bases in thetail. If a mismatch is found, then there has to be at least'-minlength' A's (or T's) past the mismatch (working from the end) forthe mismatch to be considered part of the tail. If '-mismatches' isgreater than 1 then that number of contiguous non-A (or non-T) baseswill be allowed as part of the tail. If a 5' poly-T tail is found, then the sequence will be optionallyreverse-complemented when it is written out. If a poly-A tail is reomved then '[poly-A tail removed]' is appended tothe description of the sequence. If poly-T is removed, then '[poly-Ttail removed]' is appended and if the sequence is reversed, '[reversecomplement]' is appended.
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