/[genomes]/quickload/T_parvula_May_2012/HEADER.md
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Revision 60 - (hide annotations)
Thu Sep 27 16:44:53 2018 UTC (4 years, 4 months ago) by aloraine
File size: 2406 byte(s)
Add Thellungiella parvula (salt cress) v2, May 2012 genome assembly
1 aloraine 60 <html>
2     <body>
3     <h1>Welcome</h1>
4     <p>
5     The data files listed below are formatted for visualization in the
6     Integrated Genome Browser, available from <a
7     href="https://bioviz.org">BioViz.org</a>.
8     </p>
9     <p>
10     Data files are from <a href="http://www.thellungiella.org">thellungiella.org</a>. Files were downloaded in December 2012 and reformatted for visualization in IGB.
11     </p>
12     <p>
13     For information about the genome sequence and annotations, please
14     contact Maheshi Dassanayake and Dong-Ha Oh. For information about this QuickLoad site or Integrated Genome Browser, contact Ann Loraine.
15     </p>
16     <p>
17     The genome sequence and annotations for Thellungiella parvula (common
18     name Anatolian cress) were published in the journal Nature Genetics
19     in 2011. See: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21822265">The genome of the extremophile crucifer Thellungiella parvula</a>.
20     </p>
21     <h2>About the files</h2>
22     <p>
23     Files with extension .gz were compressed and indexed using bgzip and
24     tabix tools from Heng Li.
25     </p>
26     <p>
27     The BED file T_parvula_May_2012.bed.gz is BED14 (bed detail) format,
28     developed originally in the UCSC Genome Bioinformatics group and described on their site.
29     </p>
30     <p>
31     In IGB, BED14 field 13 is designated
32     the "gene name" field and field 14 is desigated as the description
33     field. Both can be searched using the coordinates box or the Search
34     tab once the file is loaded into IGB.
35     </p>
36     <p>
37     T_parvula_May_2012.bed.gz was created from TpV84_ORFs.gff from
38     thellungiella.org. In this case, BED14 fields 13 and 4 are identical
39     and field 14 contains the Note attribute from the GFF extra feature
40     field. The time stamp of the GFF file we used was Dec. 28, 2011 and
41     the file was downloaded in Dec. 2012. The original file contained
42     transcriptional start site and polyadenylation signals that were not
43     included in the reformatted BED file because the format does not
44     support these feature types except as field 2, which represents the start of
45     transcription for a gene model. Boundaries of CDS, five_prime_UTR, and
46     three_prime_UTR features were used to delimit exon boundaries in the
47     BED output. For information about software used to perform the format
48     conversion, please see log messages associated with this file.
49     </p>
50     <p>
51     The .2bit file contains the genome sequence for parvula assembly
52     version 2, released May, 2012. The fasta file was converted to .2bit
53     format using Jim Kent's faToTwoBit tool.
54     </p>
55     </body>
56     </html>

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