BIOC0030 (BIOC3014) - Bioinformatics Workshop

In mammalian genes, polyadenylation sites are usually preceded by AATAAA or ATTAAA ~20 bases before the cleavage site and followed by a more weakly conserved GT-based motif.

Computationally, these motifs are trivial to find, but they only function in the right context. This is harder to define and includes regulation by upstream splicing factors.

It is important to remember that there should not be an in-frame stop codon in an internal exon i.e. the true termination of translation will be in the last exon. (As with every rule in Biology, there are exceptions!)

Follow the instructions below to look for potential poly-adenylation sites in your sequence

The POLYAH Server

Visit the POLYAH server at http://www.softberry.com/berry.phtml?topic=polyah&group=programs&subgroup=promoter
Click the [Help] button to get information on the likely prediction accuracy.
Click the browser's back button to return to the server.
Cut and paste the query sequence into the sequence box and press the PROCESS button to submit the job.

NOTE! As of 2018, Softberry are limiting the number of queries that may be run in one day. If you do not get a result back, then you can access the results here.

After a few seconds the results will be returned. How many candidate sites were found?

Finding Poly-adenylation sites

The POLYAH Server