I have mined some gene families from a genome. I am getting some genes with high sequence similarities however they are residing at the different position on the chromosome. So my query is that whether they can addressed as alternatively spliced variants or copy number of that particular gene family or can be considered as different gene family. kindly suggest.
Chet Ram
Hi Chet
Splice variants refer to products from the same locus that are processed differently from pre-mRNA to mRNA., So you can not find them at different positions in the chromosome.
Whether they are the same or different gene families should be easy to decide based on sequence and homology to other sequences/proteins. Check out for no-sense muations as they would be indicative of pseudogenes
Hope this helps
Hi Chet Ram,
For splice site/junction identification using raw reads friendly tools are HMMSPlicer, MapSlice.
Exons could be distributed anywhere across the chromosome. Secondly there are also psudo gens with a similar sequence.
The multi-domain proteins can have membership in more than one family, depending on their inter acting partners and functions. Good gene family classifier tool is Orthocl and be specific about similarity> 70 % and low evalues while assigning membership
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