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Revision 62 - (show annotations)
Thu Sep 27 16:53:23 2018 UTC (3 years, 7 months ago) by aloraine
File size: 3542 byte(s)
Add 12X March 2010 wine grape draft genome Vitis vinifera genome assembly
1 <h1>Vitis vinifera 12x genome assembly</h1>
2 <body>
3 <p>
4 This directory contains annotation and sequence data files from the grape 12x genome assembly released in March 2010. Files are formatted for visualization in <a href="https://bioviz.org">Integrated Genome Browser</a> (IGB).
5 </p>
6 <p>
7 Files include:
8 </p>
9 <p>
10 <ul>
11 <li>
12 2bit file - sequence file in two-bit format, created using
13 faToTwoBit.
14 When users click <b>Load Sequence</b> buttons, IGB retrieves sequence data from this file. The 2bit file name must match the genome version.
15 To obtain a copy of faToTwoBit, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
16 </li>
17 <li>
18 annots.xml - meta-data file that lists available data sets and specifies how they will look once loaded into <a href="https://bioviz.org">Integrated Genome Browser</a>.
20 <li>genome.txt - meta-data file that lists genomic sequences and their sizes, created using twoBitInfo using the 2bit file. To obtain a copy of twoBitInfo, visit <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>
22 <li>reference gene model annotations in bed or bed detail format, compressed using bgzip and indexed using tabix (See: <a href="http://bioinformatics.oxfordjournals.org/content/27/5/718">Tabix: fast retrieval of sequence features from generic TAB-delimited files</a> and <a href="http://genome.ucsc.edu/FAQ/FAQformat.html">http://genome.ucsc.edu/FAQ/FAQformat.html</a>.)
23 </ul>
24 </p>
25 <p>
26 <b>Note:</b> Gene model annotation files have been re-formatted for fast transfer over the internet and for visualization in IGB. Gene model annotation files use BED-detail format, which is the same as BED12 but contains two additional fields: field 13 contains the locus identifier and field 14 contains descriptive text.
27 </p>
28 <p>Gene model annotation files include:
29 <ul>
31 <li>V2.1.bed.gz - protein and non-protein coding gene models obtained
32 from the University of Padua <a href="http://genomes.cribi.unipd.it/grape/">CRIBI Genomics Grape
33 Genome</a> portal. These gene models load automatically when you
34 select the grape genome in IGB. These data are based on RNA-Seq
35 analysis and so probably you should use these for high-throughput
36 analysis. Gene structure annotations were downloaded April 2015 from
37 <a href="http://genomes.cribi.unipd.it/DATA/V2/V2.1/">http://genomes.cribi.unipd.it/DATA/V2/V2.1/</a>
38 as file V2.1.gff3 and descriptive text was downloaded from <a href="http://genomes.cribi.unipd.it/DATA/V2/annotation/">http://genomes.cribi.unipd.it/DATA/V2/annotation/</a> as file TopBlast.txt. The description field from TopBlast.txt was used to generate field 14 in the BED-detail file.
40 <li>V_vinifera_Mar_2010.bed.gz - protein-coding gene models obtained from Phytozome. Gene structures are from gff3 files and descriptions are from Vvinifera_145_annotation_info.txt.gz, from Phytozome. These annotations are older, contain no splice variants, and do not have (so far as we know) useful functional annotations. They are here mainly for reference. We recommend not using these for high-throughput analysis.
42 </ul>
43 <p>
44 For more information about quickload, visit <a href="http://www.bioviz.org/igb">bioviz.org/igb</a> and visit the on-line, searchable IGB User's Guide.
45 </p>
46 <p>
47 All files, except RNA-Seq data sets, are version controlled in publicly-accessible subversion repository <a href="https://svn.transvar.org/repos/genomes/trunk/pub/quickload">https://svn.transvar.org/repos/genomes/trunk/pub/quickload</a>.
48 </p>
49 </body>

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