/[genomes]/quickload/S_lycopersicum_Feb_2014/HEADER.md
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Contents of /quickload/S_lycopersicum_Feb_2014/HEADER.md

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Revision 55 - (show annotations)
Thu Sep 27 16:03:02 2018 UTC (7 months, 3 weeks ago) by aloraine
File size: 1308 byte(s)
Add Solanum lycopersicum (tomato) May 2012/SL2.40 and Feb 2014/SL2.50 genome assemblies and annotations
1 <html>
2 <body>
3 <title>IGB QuickLoad site for the tomato Solanum lycopersicum</title>
4 <h1>Solanum lycopersicum, ITAG 2.4</h1>
5 <p>
6 The data files listed below are for visualization in the Integrated Genome
7 Browser, available from <a href="https://bioviz.org">BioViz.org</a>.
8 </p>
9 <p>
10 Sequence (.2bit) and gene models (.bed.gz) data files were re-formatted from files downloaded in April, 2014 from the <a href="http://solgenomics.net/organism/Solanum_lycopersicum/genome">SolGenomics Web site</a>. The sequence data were from the ITAG2.4 release of the tomato genome.
11 </p>
12 <p>
13 In August, 2015, we added sequence and gene model annotations for the tomato plastid genome sequence obtained from GenBank accession NC_007898.3. For details, see <a href="https://bitbucket.org/lorainelab/tomato_chloroplast">this BitBucket repository</a>.
14 </p>
15 <p>
16 Files with extension .gz were compressed and indexed using bgzip and
17 tabix tools from Heng Li.
18 </p>
19 <p>
20 The .2bit file was converted from fasta to .2bit format using the faToTwoBit converter from Jim Kent. The genome.txt file was created using twoBitInfo, also from Jim Kent. Executables for these and other tools from Jim Kent are available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a>.
21 </p>
22 </body>
23 </html>

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