This directory contains the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly of the turkey genome
(melGal1, TGC (NCBI Project ID: 10805, Accession: GCA_000146605.1)), as well as repeat annotations and GenBank sequences.
This assembly was produced by the Turkey Genome Consortium.
For more information on the turkey genome, see the project website:
http://www.vtnews.vt.edu/articles/2010/09/090810-cals-genome.html
http://www.ncbi.nlm.nih.gov/bioproject/10805
Files included in this directory:
melGal1.2bit - contains the complete turkey/melGal1 genome sequence
in the 2bit file format. 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
melGal1.agp.gz - Description of how the assembly was generated from
fragments.
melGal1.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.
melGal1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
melGal1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting. RepeatMasker version: June 30 2010 (open-3-2-9)
RepeatMasker library version: 20090604
melGal1.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 - Turkey 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 - Turkey mRNA from GenBank. 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.
melGal1.chrom.sizes - Two-column tab-separated text file containing assembly
sequence names and sizes.
melGal1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
- to construct the GC Percent track
melGal1.gc5Base.wig.gz - wiggle database table for the GC Percent track
- this is an older standard alternative to the current
- bigWig format of the track, sometimes usefull for analysis
melGal1.gc5Base.wib - binary data to correspond with the gc5Base.wig file
see also: http://genome.ucsc.edu/goldenPath/help/wiggle.html
and http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
for a discussion of how to use the wig.gz and .wib files for
interaction with the GC percent data values
melGal1.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/melGal1/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/melGal1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/melGal1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/melGal1/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 -
melGal1.chrom.sizes 2010-11-04 12:07 115K
melGal1.gc5Base.wigVarStep.gz 2010-11-04 12:09 477M
melGal1.2bit 2010-11-05 12:16 257M
melGal1.agp.gz 2011-03-08 19:40 3.9M
melGal1.fa.out.gz 2011-03-08 19:40 10M
melGal1.trf.bed.gz 2011-03-08 19:40 1.0M
melGal1.fa.gz 2011-03-08 19:44 290M
melGal1.fa.masked.gz 2011-03-08 19:49 267M
melGal1.gc5Base.wib 2019-01-17 14:48 185M
melGal1.gc5Base.wig.gz 2019-01-17 14:48 4.2M
md5sum.txt 2019-01-17 15:55 479
mrna.fa.gz 2019-10-17 11:25 117K
mrna.fa.gz.md5 2019-10-17 11:25 45
xenoMrna.fa.gz 2019-10-17 11:36 6.8G
xenoMrna.fa.gz.md5 2019-10-17 11:36 49
est.fa.gz 2019-10-17 11:41 4.0M
est.fa.gz.md5 2019-10-17 11:41 44
xenoRefMrna.fa.gz 2019-10-17 11:41 331M
xenoRefMrna.fa.gz.md5 2019-10-17 11:41 52
upstream1000.fa.gz 2019-10-17 11:41 640K
upstream1000.fa.gz.md5 2019-10-17 11:41 53
upstream2000.fa.gz 2019-10-17 11:41 1.2M
upstream2000.fa.gz.md5 2019-10-17 11:41 53
upstream5000.fa.gz 2019-10-17 11:41 2.9M
upstream5000.fa.gz.md5 2019-10-17 11:41 53
genes/ 2020-10-02 13:38 -
melGal1.chromAlias.txt 2022-09-08 14:13 298K
melGal1.chromAlias.bb 2022-09-08 14:13 1.6M