This directory contains alignments of the D. melanogaster assembly (dm1, Jan. 2003) to the D. yakuba assembly (droYak1, Apr. 2004). Files included in this directory: - axtChrom directory: contains the axt alignments generated by blastz, in one file per chromosome. Blastz output was converted to lav format, which was then converted to axt format. - melanogaster.chain.zip: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html. - melanogaster.net.zip: "net" file that describes rearrangements between the species and the best D. melanogaster match to any part of the D. yakuba genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html. - md5sum.txt: checksums of the files in this directory The alignments in the axtNet directory are in "axt" format. For a description, see http://genome.ucsc.edu/goldenPath/help/axt.html. The alignments were produced by the blastz alignment program, which is available from Webb Miller's lab at Penn State University (http://www.bx.psu.edu/miller_lab/). The blastz scoring matrix used was: A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 with a gap open penalty of 400 and a gap extension penalty of 30. Each chromosome was divided into 10,010,000 base chunks with 10,000 bases of overlap. The .lav format blastz output, which does not include the sequence, was converted to .axt with lavToAxt. ----------------------------------------------------------------- If you plan to download a large file or multiple files from this directory, we recommend you use ftp rather than downloading the files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to the directory goldenPath/droYak1/vsDm1. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) All the files in this directory are freely available for public use.
Name Last modified Size Description
Parent Directory - axtChrom.zip 2004-08-04 13:58 129M md5sum.txt 2004-08-04 13:58 159 melanogaster.chain.zip 2004-05-27 12:51 20M melanogaster.net.zip 2004-05-27 12:51 11M