This directory contains the Jul. 2008 assembly of the zebra finch genome (taeGut1, WUSTL v3.2.4), as well as repeat annotations and GenBank sequences. This assembly was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine. For more information on the zebra finch genome, see the project website: http://genome.wustl.edu/genome.cgi?GENOME=Taeniopygia%20guttata Files included in this directory: taeGut1.2bit - contains the complete zebra finch/taeGut1 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 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 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. 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 - Zebra finch ESTs in GenBank. This sequence data is updated once a week via automatic GenBank updates. taeGut1.quals.fa.gz - quality scores in fasta file format md5sum.txt - checksums of files in this directory mrna.fa.gz - Zebra finch mRNA from GenBank. This sequence data is updated once a week via automatic GenBank updates. refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updated once a week via automatic GenBank updates. upstream1000.fa.gz - Sequences 1000 bases upstream of annotated transcription starts for RefSeq genes with annotated 5' UTRs. This file is updated weekly so it could be slightly out of sync with the 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. taeGut1.chrom.sizes - Two-column tab-separated text file containing assembly sequence names and sizes. taeGut1.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/taeGut1/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/taeGut1/bigZips/ . For a single file, e.g. chromFa.tar.gz rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/bigZips/chromFa.tar.gz . Or with wget, all files: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/bigZips/*' With wget, a single file: wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/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 Zebra finch sequence is made freely available to the community by the Genome Sequencing Center, Washington University School of Medicine, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of these data are properly acknowledged. See http://genome.wustl.edu/data.cgi for credit information. 3. The centers producing the data reserve the right to publish the initial large-scale analyses of the data set, including large-scale identification of regions of evolutionary conservation and large-scale genomic assembly. Large-scale refers to regions with size on the order of a chromosome. 4. This is in accordance with, and with the understandings in the Fort Lauderdale meeting discussing Community Resource Projects (see http://www.wellcome.ac.uk/doc_wtd003208.html) and the resulting NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537). 5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory - chromAgp.tar.gz 2008-08-06 15:25 2.8M chromFa.tar.gz 2008-08-06 15:32 383M chromFaMasked.tar.gz 2008-08-06 15:37 319M chromTrf.tar.gz 2008-08-06 15:37 2.0M est.fa.gz 2019-10-17 22:20 21M est.fa.gz.md5 2019-10-17 22:20 44 genes/ 2020-02-05 13:47 - md5sum.txt 2013-12-11 10:46 305 mrna.fa.gz 2019-10-17 22:05 1.3M mrna.fa.gz.md5 2019-10-17 22:05 45 refMrna.fa.gz 2019-10-17 22:21 438K refMrna.fa.gz.md5 2019-10-17 22:21 48 taeGut1.2bit 2008-08-05 18:52 352M taeGut1.chrom.sizes 2008-08-05 15:34 1.2K taeGut1.chromAlias.txt 2020-09-29 10:49 1.1K taeGut1.fa.gz 2020-01-23 02:26 384M taeGut1.quals.fa.gz 2009-06-09 10:40 273M upstream1000.fa.gz 2019-10-17 22:21 216K upstream1000.fa.gz.md5 2019-10-17 22:21 53 upstream2000.fa.gz 2019-10-17 22:21 418K upstream2000.fa.gz.md5 2019-10-17 22:21 53 upstream5000.fa.gz 2019-10-17 22:21 1.0M upstream5000.fa.gz.md5 2019-10-17 22:21 53 xenoMrna.fa.gz 2019-10-17 22:15 6.8G xenoMrna.fa.gz.md5 2019-10-17 22:16 49 xenoRefMrna.fa.gz 2019-10-17 22:21 330M xenoRefMrna.fa.gz.md5 2019-10-17 22:21 52