Hi Padraig, I queried our engineers and got this list of recommendations for you:
1) Aligning all genbank mRNAs from Chinese Hamster 2) Aligning all of their own transcriptome data 3) Aligning all of genbank ESTs from Chinese Hamster 4) Mapping human proteins as derived from either the UCSC gene set or RefSeq 5) Mapping mouse proteins from UCSC or RefSeq 6) Doing a multiple species genome alignment with mouse, rat, rabbit, dog, elephant, opossum, platypus, chicken. Do pairwise alignments as well. 7) Mine the genomic reads and transcriptomic reads for SNPs. Be careful not to call recently duplicated and only slightly diverged regions slight divergences as SNPs though. 8) Run several repeat finders. 9) Run a CpG island detector. 10) Run a good gene prediction program like Augustus. 11) Try to find a wet lab group willing to do some DNAse assays.... I hope this is helpful. Good luck with your work! -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/9/11 1:25 AM, padraig doolan wrote: > 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 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
