I would be interested to use a script for detecting exon duplications in given sequence. The duplications may not necessarily match 100% the region which was duplicated. Thus, the definition of a treshould of sequence similarity for the duplications would be appreciated.
Andre, I've been thinking a dot plot should show up duplications as lines off the axis of self-identity, but I don't have a script yet. Paul
I know of ASTALAVISTA program that can extract all alternative spliced events. As such it can be used to detect exonic and intrinic splice variants, if that's what you are trying to do. The source code and relevant information for ASTALAVISTA is here...http://sammeth.net/confluence/pages/viewpage.action?pageId=5177667
git clone http://sammeth.net/bitbucket/scm/barna/barna.git
If you have many sequences and need to automate the process, running BLAST with the sequence against itself, for example with blast2seq (http://nebc.nox.ac.uk/bioinformatics/docs/bl2seq.html) is useful. If you choose one of the tabular output formats, getting the positions of the duplications should not be too difficult.
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