I would start from BioMart. I’m also working on OR (albeit insect ones). Try also MGI (Mouse Genome Informatics). Starting from mouse Ors you can scoop orthologs in other mammalian species.
On 22 May 2015, at 18:44, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi James,
Your questions are more about bioinformatics project design rather than Chimera use.
Chimera provides basic BLAST searching of NCBI’s “nr” and “pdb” sequence databases, but these are the same databases generally used by BLAST whether you use it from Chimera or from another program, or stand-alone. Also, Chimera can fetch specific individual sequences from UniProt based on UniProt identifier, but that isn’t searching, it is just getting data you already knew you wanted.
I believe NCBI’s “nr” and UniProtKB are both meant to be comprehensive (cover “all” sequences) but in their own ways, and you would have to go to those resources or their publications to learn the details. There are probably also specialized GPCR and/or olfactory receptor sequence databases. Then there are multiple ways of searching, with individual sequences or with derived patterns such as hidden Markov Models (HMMs). This is a really broad topic and in my opinion, beyond the scope of this forum. You’ve probably done some of this already, but I would recommend reading similar studies in quality journals by authors you respect, to see how they have designed their projects.
Chimera doesn’t have HMM-related tools or evolutionary trace, it just allows conservation analysis on your whole alignment, or subsets of that alignment opened in separate windows.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On May 22, 2015, at 9:22 AM, James Starlight <jmsstarlight@gmail.com> wrote:
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
dramatically.
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!
James
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