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Revision 43 - (hide annotations)
Thu Sep 27 15:15:02 2018 UTC (5 years, 8 months ago) by aloraine
File size: 2189 byte(s)
Add Oryza sativa japonica June 2009 and Oryza sativa japonica variety Os-Nipponbare-Reference-IRGSP-1.0 genome assemblies and annotations
1 aloraine 43 <h1>Oryza sativa japonica genome assembly</h1>
2     <body>
3     <p>
4     This directory contains annotation and sequence data files from rice genome assembly Os-Nipponbare-Reference-IRGSP-1.0 released October 2011. 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="http://bioviz.org/igb">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.
27     </p>
28     <p>Gene model annotation files include:
29     <ul>
30     <li>O_sativa_japonica_Oct_2011.bed.gz - RGAP/MSU7 gene models, from the <a href="http://rice.plantbiology.msu.edu">Rice Genome Annotation Project</a> at MSU.
31     <li>IRGSP-1.0_representative_2013-04-24.bed.gz - From the Rice Annotation Project Database <a href="http://rapdb.dna.affrc.go.jp/">RAP-Db</a>.
32     </ul>
33     <p>
34     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.
35     </p>
36     </body>

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