[Chimera-users] On the seeking of the orthologs

James Starlight jmsstarlight at gmail.com
Fri May 22 09:22:47 PDT 2015

Dear Chimera users!

I'd like to ask some suggestion regarding my bioinformatician task and
possible ways of its realisation using some bioinformatics methods
implemented in Chimera.

1)I need to seek for some sequence database (here I don't know
absolutely how to do it) of the olfactory receptors and to select 10
sequences of the Ors corresponded to 10 different mammalian species ->
according to my idea it should be very different species associated
with different ecological niches so its olfactory spectrum should vary
Here the question: in what DB such search should be better with the
inclusion of flexible search criteria's like what I've listened above?

2)After allocating of those 10 sequences I should to find *all*
possible orthologs against them-> to find all OR in another species
which have conservation degree agains target above chosen threshold .
Eventually I'll need to make some analysis regarding overall
conservation of the OR within different species and to point out what
OR are most important (conservative) in different organisms in
accordance to some pre-defined criteria's (i.e ecological niche of the
species because it's associated with the odor spectrum). Here the
question: would the methods like blast-search be enough for such task
or I should to use also methods like evolutional tracing (to find all
important residues in different OR which tend to co-evaluate) based on
its alignment data?

I would be very thankful for any suggestion!


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