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.

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[TXT]README.txt20-Feb-2015 15:32 3.1K 
[TXT]README.txt.bak06-May-2014 16:01 3.0K 
[   ]anoGam1.2bit08-Jun-2004 15:43 70M 
[   ]anoGam1.chrom.sizes07-Jun-2004 17:40 99  
[TXT]md5sum.txt05-May-2014 15:32 286  

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