Hi Padraig, Unfortunately your question is beyond the scope of this mailing list as we do not provide advice regarding scientific direction, but focus on browser usage issues.
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 1/5/2012 5:07 AM, padraig doolan wrote: > Dear Brooke, > > Thanks for your very informative response, it was very helpful. > Apologies also for the delay in responding; the University here had a > lot of campus-wide email outages in weeks approaching christmas and we > were without email access for several weeks prior to the holidays. > > I was also wondering if you could help me with an associated issue; we > are interested in using the newly available chinese hamster ovary > (CHO) genome information to generate a commercially-available > microarray chip and I was wondering; what are the steps that would be > required in constructing a CHO chip from that data? For instance, > > * How well assembled would the sequence need to be? > * Level of annotation? > > Best regards, > Padraig > > On 14/12/2011 18:55, Brooke Rhead wrote: >> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
