Dear UCSC Genome Bioinformatics,
My name is Padraig Doolan and I am the Program Leader for Expression
Microarrays and Bioinformatics at the National Institute for Cellular
Biotechnology (NICB), Ireland (www.nicb.ie/). We are a publicly-funded
basic science research institute.
Our small bioinformatics group are just starting the process of
analysisng a new genome (and transcriptome) for the Chinese Hamster
Ovary (CHO) cell line which was recently published (Xu et al., The
genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat
Biotechnol. 2011 Jul 31;29(8):735-41. doi: 10.1038/nbt.1932.) by another
group. We do a lot of functional work on this organism and we're looking
for some good guidelines (published papers, online resources, etc.)
which might help us map out some achievable goals with regard to the
in-silico characterisation of this genome.
For example, after the sequence is published, what are the next step(s)
in providing relevant information? Lists of SNPs? Predicted
proteome/secretome/numbers of predicted protein types (e.g.
kinases/g-coupled/nuclear-/membrane-localised), etc.?
I'm looking through the Human Genome Project Publications list
(http://www.ornl.gov/sci/techresources/Human_Genome/publicat/publications.shtml)
for inspiration, but this type of analysis output is relatively new for
our group (we are usually more focussed on translational medicine). Is
there any recommended guidelines your institute can suggest for
following in the footsteps of the HGP in in silico analysis of novel
genomes/transcriptomes? Can your organisation suggest a couple of key
papers or maybe a good analysis strategy?
Best regards,
Padraig Doolan
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