This directory contains the Mar. 2006 assembly of the lancelet genome
(UCSC version braFlo1; JGI v.1.0, March 2006), repeat annotations, and
GenBank sequences.
This assembly was produced by the US DOE Joint Genome Institute (JGI).
For more information on the lancelet genome, see the project website at
http://genome.jgi-psf.org/Brafl1/Brafl1.info.html.
Files included in this directory:
braFlo1.2bit - contains the complete lancelet/braFlo1 genome sequence
in the 2bit file format. Repeats from WindowMasker 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.tar.gz - Description of how the assembly was generated from
fragments, unpacking to one file per chromosome.
chromFa.tar.gz - The assembly sequence in one file per chromosome.
Repeats from WindowMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case.
chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.
Not available: chromOut.tar.gz - there is no repeat masker data for this
genome. In place of repeat masker, there is the WindowMasker output:
chromWMSdust.bed.gz - bed file for chrUn and chrM used as repeat areas
identified by WindowMasker with the -sdust option.
chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
with period less than or equal to 12, and translated into UCSC's BED
format (one file per chromosome).
est.fa.gz - Lancelet 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 - Lancelet 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.
braFlo1.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/braFlo1/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/braFlo1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/bigZips/chromFa.tar.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/bigZips/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/braFlo1/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 lancelet sequence is made freely available before scientific publication
by the JGI. Please see the JGI data release policy at
http://genome.jgi-psf.org/Brafl1/Brafl1.download.html for usage restrictions
and citation information.
Name Last modified Size Description
Parent Directory -
braFlo1.chrom.sizes 2007-03-26 10:30 27
chromAgp.tar.gz 2008-05-01 14:06 71K
chromFa.tar.gz 2008-05-01 14:10 265M
chromFaMasked.tar.gz 2008-05-01 14:13 204M
chromTrf.tar.gz 2008-05-01 14:13 1.5M
chromWMSdust.bed.gz 2008-05-28 15:55 37M
braFlo1.2bit 2008-05-28 16:02 254M
md5sum.txt 2014-02-04 08:50 305
mrna.fa.gz 2019-10-14 21:18 12M
mrna.fa.gz.md5 2019-10-14 21:18 45
xenoMrna.fa.gz 2019-10-14 21:27 6.8G
xenoMrna.fa.gz.md5 2019-10-14 21:27 49
est.fa.gz 2019-10-14 21:31 69M
est.fa.gz.md5 2019-10-14 21:31 44
xenoRefMrna.fa.gz 2019-10-14 21:32 331M
xenoRefMrna.fa.gz.md5 2019-10-14 21:32 52
upstream1000.fa.gz 2019-10-14 21:32 214K
upstream1000.fa.gz.md5 2019-10-14 21:32 53
upstream2000.fa.gz 2019-10-14 21:32 433K
upstream2000.fa.gz.md5 2019-10-14 21:32 53
upstream5000.fa.gz 2019-10-14 21:32 1.1M
upstream5000.fa.gz.md5 2019-10-14 21:32 53
braFlo1.fa.gz 2020-01-23 02:20 265M