This directory contains the Feb. 2003 assembly of the A. gambiae
genome (anoGam1) from the International Anopheles Genome Project
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
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
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
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
xenoMrna.fa.gz - GenBank mRNAs from species other than that of
the genome. This sequence data is updated once a week via automatic
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.
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80