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 - est.fa.gz 2020-02-28 15:47 23M est.fa.gz.md5 2020-02-28 15:47 44 md5sum.txt 2014-01-27 16:05 358 mrna.fa.gz 2020-02-28 15:33 563K mrna.fa.gz.md5 2020-02-28 15:33 45 petMar1.2bit 2008-01-28 14:39 287M petMar1.agp.gz 2008-04-29 13:56 5.7M petMar1.chrom.sizes 2008-01-27 08:15 1.8M petMar1.fa.gz 2008-04-29 14:00 270M petMar1.fa.masked.gz 2008-04-29 14:03 179M petMar1.fa.out.gz 2008-04-29 13:56 8.2M petMar1.quals.fa.gz 2009-06-09 10:39 332M petMar1.trf.bed.gz 2008-04-29 13:56 2.0M refMrna.fa.gz 2020-02-28 15:47 20 refMrna.fa.gz.md5 2020-02-28 15:47 48 upstream1000.fa.gz 2020-02-28 15:48 66K upstream1000.fa.gz.md5 2020-02-28 15:48 53 upstream2000.fa.gz 2020-02-28 15:48 115K upstream2000.fa.gz.md5 2020-02-28 15:48 53 upstream5000.fa.gz 2020-02-28 15:49 233K upstream5000.fa.gz.md5 2020-02-28 15:49 53 xenoMrna.fa.gz 2020-02-28 15:42 6.8G xenoMrna.fa.gz.md5 2020-02-28 15:42 49 xenoRefMrna.fa.gz 2020-02-28 15:47 337M xenoRefMrna.fa.gz.md5 2020-02-28 15:47 52