Hi Miguel, If you are asking for whole-genome multi-fasta alignments of D. simulans to D. melanogaster, we don't have exactly that, but we do have those alignments in the AXT format (see http://genome.ucsc.edu/goldenPath/help/axt.html).
The files are in http://hgdownload.cse.ucsc.edu/goldenPath/dm3/vsDroSim1/axtNet/. Here is how to navigate to that directory from http://genome.ucsc.edu/: click the Downloads link in the left sidebar. Click on the D. melanogaster link in the Insects section. Then you should see a section for Apr. 2006 (dm3) which is BDGP release 5, with a list of pairwise alignments. Click on D. melanogaster/D. simulans (droSim1), and then the axtNet link. If you prefer ftp then you can use the same URLs but with ftp:// instead of http:// to download the axt files. Hope that helps, Angie ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "Miquel Ramia" <[email protected]> > Cc: [email protected] > Sent: Thursday, December 3, 2009 10:59:23 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] whole fasta alignment > > Hello, > > The question is a bit difficult to interpret. Here are some potential > answers - but write back with more details if none of these address > what you are asking for. > > If you want the genomic sequence, one fasta record per chromosome, the > data is available via ftp from our downloads server. Here are some > links to the instructions: > http://genome.ucsc.edu/FAQ/FAQdownloads#download1 > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download > > If you want genome alignments (FlyBase, etc), the alignments are > organized per query transcript, but can be organized by chromosome if > extracted from the Table browser or created from the files on the > Downloads server. > > If you instead are referring to the Comparative alignments (one genome > vs another) or the Conservation data (multiple genomes), the data is > organized by multiple-alignment block, but it can also be grouped by > chromosome (the blocks are not continuous) and extracted from the > Table browser or created from files on the Downloads server. > > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser > > Again, please write back to clarify if is not the information you are > looking for, > Jennifer > > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "Miquel Ramia" <[email protected]> wrote: > > > From: "Miquel Ramia" <[email protected]> > > To: [email protected] > > Sent: Thursday, December 3, 2009 7:51:12 AM GMT -08:00 US/Canada Pacific > > Subject: [Genome] whole fasta alignment > > > > Hi, > > > > We are interested in the d.melanogaster-d.simulans alignment. We've seen > > that using the browser you can see the sequences continuously, but you > > only can download little alignments instead. We wonder if there is a > > way to get the whole alignment in one sequence for each specie (for each > > chromosome) and not divided in small parts. > > > > kind regards. > > > > -- > > > > Miquel Ràmia > > > > > > > > _______________________________________________ > > 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
