This directory contains the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)
assembly of the panda genome (ailMel1, BGI-Shenzhen AilMel 1.0 Dec. 2009),
as well as repeat annotations and GenBank sequences.

This assembly was produced by the BGI-Shenzhen sequencing center,
Beijing Genomics Institute at Shenzhen.

For more information on the panda genome, see the project website:

Files included in this directory:

ailMel1.2bit - contains the complete panda/ailMel1 genome sequence
    in the 2bit file format.  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:
    See also:

ailMel1.agp.gz - Description of how the assembly was generated from

ailMel1.fa.gz - "Soft-masked" assembly sequence in one file.
    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.

ailMel1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

ailMel1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the

ailMel1.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED

est.fa.gz - Panda ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Panda 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

upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
    transcription starts of RefSeq genes with annotated 5' UTRs.
    This file is updated weekly so it might be slightly out of sync with
    the RefSeq data which is updated daily for most assemblies.

upstream2000.fa.gz - Same as upstream1000, but 2000 bases.

upstream5000.fa.gz - Same as upstream1000, but 5000 bases.

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.

ailMel1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

ailMel1.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

If you plan to download a large file or multiple files from this
directory, we recommend that you use ftp rather than downloading the
files via our website. To do so, ftp to
[username: anonymous, password: your email address], then cd to the
directory goldenPath/ailMel1/bigZips. To download multiple files, use
the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)

Alternate methods to ftp access.

Using an rsync command to download the entire directory:
    rsync -avzP rsync:// .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -O chromFa.tar.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz
      Name                    Last modified      Size  Description
Parent Directory - xenoRefMrna.fa.gz.md5 2019-10-14 19:34 52 xenoRefMrna.fa.gz 2019-10-14 19:34 331M xenoMrna.fa.gz.md5 2019-10-14 19:30 49 xenoMrna.fa.gz 2019-10-14 19:29 6.8G upstream5000.fa.gz.md5 2019-10-14 19:35 53 upstream5000.fa.gz 2019-10-14 19:35 20 upstream2000.fa.gz.md5 2019-10-14 19:35 53 upstream2000.fa.gz 2019-10-14 19:35 20 upstream1000.fa.gz.md5 2019-10-14 19:34 53 upstream1000.fa.gz 2019-10-14 19:34 20 refMrna.fa.gz.md5 2010-04-05 16:48 48 refMrna.fa.gz 2010-04-05 16:48 692K mrna.fa.gz.md5 2019-10-14 19:20 45 mrna.fa.gz 2019-10-14 19:20 34K md5sum.txt 2010-05-20 16:26 510 genes/ 2020-10-02 13:36 - est.fa.gz.md5 2019-10-14 19:34 44 est.fa.gz 2019-10-14 19:34 415 ailMel1.trf.bed.gz 2010-04-01 13:58 4.1M ailMel1.fa.out.gz 2010-04-01 13:58 121M ailMel1.fa.masked.gz 2010-04-01 14:23 448M ailMel1.fa.gz 2010-04-01 14:14 713M ailMel1.chromAlias.txt 2022-09-08 14:00 3.7M 2022-09-08 14:00 17M ailMel1.chrom.sizes 2010-02-02 16:05 1.2M ailMel1.agp.gz 2010-04-01 13:57 3.6M ailMel1.2bit 2010-02-03 09:38 577M