As usual, Chris is more eloquent than I. Nutshell is that you want to specialize the analysis to the specific scientific/biological/chemical/physical problem you are thinking of. Joe On Thu, 13 Feb 2003, Chris Dwan (CCGB) wrote: > > > ... > > 2) If I have two large genomes that need a lengthy blast, how can I > > split that up? > > ... > > Even a valid hit can have some repeat in it ... > > ... > > However, I'm after a generalized solution that doesn't require special > > knowledge of the sequences. > > ... > > Disclaimer first: I don't know if this comment applies to your > particular situation. > > So much for apologies. > > I've had several mid-sized script-n-hack projects start with exactly > this question: "How do I BLAST one genome against another?" When we > got to the root of it, the biological questions of interest demanded a > variety of approaches. Here are two examples: > > 1) Find me putative orthologs between these two chromosomes. > ---------------------------------------------------------- > - This broke down into > 1) Find the genes > 2) Find the orthologs. > > - In this case it makes a lot of sense to filter out > low complexity sequence up front, hit each chromosome > with a suite of gene-finders...including a blastx vs. > a well annotated protein dataset like swissprot. From > that, we get a set of possible genes in each chromosome. > Now the problem is more recognizable as a job that BLAST > might be good at. > > 2) Show me the large scale genomic events that provide evidence > for evolutionary relation between these two specific chromosomes. > ----------------------------------------------------------------- > - Here, we do NOT want to get rid of low complexity or repetitive > elements. A straight-ahead "overlapping chunks -> blastn -> > dot-plot" approach gives what is wanted. > > 3) Show me the paralogs (duplicated genes within a single genome) > and... > > You get the idea. > > -Chris Dwan > Center for Computational Genomics and Bioinformatics > University of Minnesota > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >