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 - braFlo1.2bit 2008-05-28 16:02 254M braFlo1.chrom.sizes 2007-03-26 10:30 27 braFlo1.fa.gz 2020-01-23 02:20 265M 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 est.fa.gz 2020-09-09 18:38 69M est.fa.gz.md5 2020-09-09 18:38 44 md5sum.txt 2014-02-04 08:50 305 mrna.fa.gz 2020-09-09 18:23 12M mrna.fa.gz.md5 2020-09-09 18:23 45 upstream1000.fa.gz 2020-09-09 18:39 225K upstream1000.fa.gz.md5 2020-09-09 18:39 53 upstream2000.fa.gz 2020-09-09 18:39 444K upstream2000.fa.gz.md5 2020-09-09 18:39 53 upstream5000.fa.gz 2020-09-09 18:39 1.1M upstream5000.fa.gz.md5 2020-09-09 18:39 53 xenoMrna.fa.gz 2020-09-09 18:34 7.0G xenoMrna.fa.gz.md5 2020-09-09 18:34 49 xenoRefMrna.fa.gz 2020-09-09 18:39 344M xenoRefMrna.fa.gz.md5 2020-09-09 18:39 52