This directory contains the Feb. 2003 assembly of the A. gambiae genome (anoGam1) from the International Anopheles Genome Project (version MOZ2). Files included in this directory: anoGam1.2bit - contains the complete A. gambiae/anoGam1 genome sequence in the 2bit file format. While we are providing the .2bit for this assembly, we will continue to use the .nib files in the Genome Browser. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case. The utility program, twoBitToFa (available from the kent src tree), can be used to extract .fa file(s) from this file. A pre-compiled version of the command line tool can be found at: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ See also: http://genome.ucsc.edu/admin/git.html http://genome.ucsc.edu/admin/jk-install.html chromAgp.zip - Description of how the assembly was generated from fragments at a chromosome layout level. chromFa.zip - The assembly sequence chromosome in one file per chromosome. Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are in lower case while non-repeating sequence is in upper case. RepeatMasker March 2004 version with RepBase libraries: RepBase Update 8.4, RM database version 20040225. chromFaMasked.zip - The assembly sequence in one file per chromosome. Repeats are masked by capital Ns and non-repeating sequence is shown in upper case. chromOut.zip - RepeatMasker .out file for chromosomes. These were done with RepeatMasker at the -s sensitive setting. chromTrf.zip - Tandem Repeats Finder locations, filtered to keep repeats with period less than or equal to 12, translated into one .bed file per chromosomes. est.fa.gz - A. gambiae ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. md5sum.txt - MD5 checksum of these files to verify correct transmission. mrna.fa.gz - A. gambiae mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. xenoMrna.fa.gz - GenBank mRNAs from species other than that of the genome. This sequence data is updated once a week via automatic GenBank updates. anoGam1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. --------------------------------------------------------------- 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/bigZips. To download multiple files, use the "mget" command: mget <filename1> <filename2> ... - or - mget -a (to download all the files in the directory) The A. gambiae sequence is made freely available by The International Anopheles Genome Project.
Name Last modified Size Description
Parent Directory - anoGam1.2bit 2004-06-08 15:43 70M anoGam1.chrom.sizes 2004-06-07 17:40 99 anoGam1.fa.gz 2020-01-23 02:18 81M chromAgp.zip 2004-06-17 13:25 217K chromFa.zip 2004-06-17 13:28 81M chromFaMasked.zip 2004-06-17 13:30 74M chromOut.zip 2004-06-17 13:25 3.9M chromTrf.zip 2004-06-17 13:30 616K est.fa.gz 2020-02-27 16:35 31M est.fa.gz.md5 2020-02-27 16:35 44 md5sum.txt 2014-05-05 15:32 286 mrna.fa.gz 2020-02-27 16:19 16M mrna.fa.gz.md5 2020-02-27 16:19 45 xenoMrna.fa.gz 2020-02-27 16:29 6.8G xenoMrna.fa.gz.md5 2020-02-27 16:30 49 xenoRefMrna.fa.gz 2020-02-27 16:35 337M xenoRefMrna.fa.gz.md5 2020-02-27 16:35 52