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	<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>