This directory contains alignments of the D. melanogaster assembly (dm1, Jan. 2003) to the A. gambiae assembly (anoGam1, Feb. 2003). Files included in this directory: - axtChrom.zip: contains the axt alignments generated by blastz. Blastz output was converted to lav format, which was then converted to axt format. - axtNet directory: contains chained and netted alignments, i.e. the best chains in the genome, with gaps in the best chains filled in by next-best chains where possible. - 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 A. gambiae 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 -90 -25 -100 C -90 100 -100 -25 G -25 -100 100 -90 T -100 -25 -90 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. The axtNet alignments were processed with chainNet, netSyntenic, and netClass written by Jim Kent at UCSC. ----------------------------------------------------------------- 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/anoGam1/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. The A. gambiae sequence is made freely available by The International Anopheles Genome Project.
Name Last modified Size Description
Parent Directory - axtChrom.zip 2004-08-20 10:54 33M axtNet/ 2004-08-23 11:12 - md5sum.txt 2004-08-20 10:56 534 melanogaster.chain.zip 2004-06-17 13:51 6.5M melanogaster.net.zip 2004-06-17 13:51 3.1M