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:
http://www.genomics.cn/en/index.php
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:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
See also:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
ailMel1.agp.gz - Description of how the assembly was generated from
fragments.
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
-s (sensitive) setting. *** PLEASE ADD REPEATMASKER VERSION AND LIB VERSION FROM THE DATE THAT REPEATMASKER WAS RUN (MAY BE IN MAKE.DOC)
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
format.
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
updates.
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 hgdownload.cse.ucsc.edu
[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://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/ailMel1/bigZips/chromFa.tar.gz'
-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 -
ailMel1.chrom.sizes 2010-02-02 16:05 1.2M
ailMel1.2bit 2010-02-03 09:38 577M
ailMel1.agp.gz 2010-04-01 13:57 3.6M
ailMel1.fa.out.gz 2010-04-01 13:58 121M
ailMel1.trf.bed.gz 2010-04-01 13:58 4.1M
ailMel1.fa.gz 2010-04-01 14:14 713M
ailMel1.fa.masked.gz 2010-04-01 14:23 448M
refMrna.fa.gz 2010-04-05 16:48 692K
refMrna.fa.gz.md5 2010-04-05 16:48 48
md5sum.txt 2010-05-20 16:26 510
mrna.fa.gz 2019-10-14 19:20 34K
mrna.fa.gz.md5 2019-10-14 19:20 45
xenoMrna.fa.gz 2019-10-14 19:29 6.8G
xenoMrna.fa.gz.md5 2019-10-14 19:30 49
est.fa.gz 2019-10-14 19:34 415
est.fa.gz.md5 2019-10-14 19:34 44
xenoRefMrna.fa.gz 2019-10-14 19:34 331M
xenoRefMrna.fa.gz.md5 2019-10-14 19:34 52
upstream1000.fa.gz 2019-10-14 19:34 20
upstream1000.fa.gz.md5 2019-10-14 19:34 53
upstream2000.fa.gz 2019-10-14 19:35 20
upstream2000.fa.gz.md5 2019-10-14 19:35 53
upstream5000.fa.gz 2019-10-14 19:35 20
upstream5000.fa.gz.md5 2019-10-14 19:35 53
genes/ 2020-10-02 13:36 -
ailMel1.chromAlias.txt 2022-09-08 14:00 3.7M
ailMel1.chromAlias.bb 2022-09-08 14:00 17M