This directory contains the Mar. 2007 assembly of the lamprey genome
(UCSC version petMar1; WUSTL v.3.0, March 2007), repeat annotations,
and GenBank sequences.
This assembly was produced by the Genome Sequencing Center at the
Washington University School of Medicine in St. Louis.
For more information on the lamprey genome, see the project website at
http://genome.wustl.edu/genome.cgi?GENOME=Petromyzon%20marinus.
Files included in this directory:
petMar1.2bit - contains the complete lamprey/petMar1 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
petMar1.agp.gz - Description of how the assembly was generated from
fragments.
petMar1.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.
petMar1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
petMar1.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the
-s (sensitive) setting.
Jan 11 2008 (open-3-1-9) version of RepeatMasker
20071204 version of RepeatMaskerLib.embl libraries
petMar1.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 - Lamprey ESTs in GenBank. This sequence data is updated once a
week via automatic GenBank updates.
petMar1.quals.fa.gz - quality scores in fasta file format
md5sum.txt - checksums of files in this directory
mrna.fa.gz - Lamprey mRNA from GenBank. This sequence data is updated
once a week via automatic GenBank updates.
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for Xeno RefSeq genes with annotated 5' UTRs.
This file is updated weekly so it could be slightly out
of sync with the Xeno 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.
petMar1.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 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/petMar1/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/petMar1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/petMar1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/petMar1/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
------------------------------------------------------------------
The Lamprey sequence is made freely available before scientific publication
by the Genome Sequencing Center, Washington University in St. Louis School of
Medicine. Please see the WUSTL data use policy at http://genome.wustl.edu/data.cgi
for usage restrictions and citation information.
Name Last modified Size Description
Parent Directory -
refMrna.fa.gz 2019-10-17 17:47 20
est.fa.gz.md5 2019-10-17 17:46 44
mrna.fa.gz.md5 2019-10-17 17:31 45
refMrna.fa.gz.md5 2019-10-17 17:47 48
xenoMrna.fa.gz.md5 2019-10-17 17:42 49
xenoRefMrna.fa.gz.md5 2019-10-17 17:47 52
upstream1000.fa.gz.md5 2019-10-17 17:47 53
upstream2000.fa.gz.md5 2019-10-17 17:48 53
upstream5000.fa.gz.md5 2019-10-17 17:48 53
md5sum.txt 2014-01-27 16:05 358
upstream1000.fa.gz 2019-10-17 17:47 62K
upstream2000.fa.gz 2019-10-17 17:48 109K
upstream5000.fa.gz 2019-10-17 17:48 212K
mrna.fa.gz 2019-10-17 17:31 557K
petMar1.chrom.sizes 2008-01-27 08:15 1.8M
petMar1.trf.bed.gz 2008-04-29 13:56 2.0M
petMar1.agp.gz 2008-04-29 13:56 5.7M
petMar1.fa.out.gz 2008-04-29 13:56 8.2M
est.fa.gz 2019-10-17 17:46 23M
petMar1.fa.masked.gz 2008-04-29 14:03 179M
petMar1.fa.gz 2008-04-29 14:00 270M
petMar1.2bit 2008-01-28 14:39 287M
xenoRefMrna.fa.gz 2019-10-17 17:47 331M
petMar1.quals.fa.gz 2009-06-09 10:39 332M
xenoMrna.fa.gz 2019-10-17 17:41 6.8G