[BiO BB] Finding introns and exons..

Ann Loraine aloraine at gmail.com
Thu Jul 13 11:04:14 EDT 2006

Greetings Hamid,

When I do this, I usually get the data from UCSC Genome Informatics
Table Browser as a "GFF" file and write some simple scripts to extract
non-redundant exons and introns. You can even use simple Unix
utilities (grep, cut, uniq) to do the first steps.

Fruit fly is actually a good choice for this because the FlyBase gene
structure annotations are relatively non-redundant - that is, the same
general gene structure is rarely included multiple times, unlike for
other data sets from other species. However, in the past I have
noticed that when multiple ORFs are associated with a gene structure,
FlyBase reports the gene structure multiple times, once per ORF. Also,
you have to be careful to filter out pseudogenes and RNA genes, if
these are not of interest.



On 7/13/06, hamid <hamid at ibb.ut.ac.ir> wrote:
> Hi buddy,
> I need to extract all introns and exons of an organism such as D.
> melanogaster.
> How can I download all of the introns and exons as a bunch?
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Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham

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