quickload/T_parvula_May_2012/HEADER.md

<html>
<body>
<h1>Welcome</h1>
<p>
The data files listed below are formatted for visualization in the
Integrated Genome Browser, available from <a
 href="https://bioviz.org">BioViz.org</a>.
</p>
<p>
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.
</p>
<p>
For information about the genome sequence and annotations, please
contact Maheshi Dassanayake and Dong-Ha Oh. For information about this QuickLoad site or Integrated Genome Browser, contact Ann Loraine. 
</p>
<p>
The genome sequence and annotations for Thellungiella parvula (common
name Anatolian cress) were published in the journal Nature Genetics
in 2011. See: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21822265">The genome of the extremophile crucifer Thellungiella parvula</a>.
</p>
<h2>About the files</h2>
<p>
Files with extension .gz were compressed and indexed using bgzip and
tabix tools from Heng Li. 
</p>
<p>
The BED file T_parvula_May_2012.bed.gz is BED14 (bed detail) format,
developed originally in the UCSC Genome Bioinformatics group and described on their site.
</p>
<p>
In IGB, BED14 field 13 is designated
the "gene name" field and field 14 is desigated as the description
field. Both can be searched using the coordinates box or the Search
tab once the file is loaded into IGB.
</p>
<p>
T_parvula_May_2012.bed.gz was created from TpV84_ORFs.gff from
thellungiella.org. In this case, BED14 fields 13 and 4 are identical
and field 14 contains the Note attribute from the GFF extra feature
field. The time stamp of the GFF file we used was Dec. 28, 2011 and
the file was downloaded in Dec. 2012. The original file contained
transcriptional start site and polyadenylation signals that were not
included in the reformatted BED file because the format does not
support these feature types except as field 2, which represents the start of
transcription for a gene model. Boundaries of CDS, five_prime_UTR, and
three_prime_UTR features were used to delimit exon boundaries in the
BED output. For information about software used to perform the format
conversion, please see log messages associated with this file.
</p>
<p>
The .2bit file contains the genome sequence for parvula assembly
version 2, released May, 2012. The fasta file was converted to .2bit
format using Jim Kent's faToTwoBit tool.
</p>
</body>
</html>
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>