Lena Week 11 - Revision history

Lena: added category

2013-11-14T17:46:53Z

added category

Lena: /* Model Organism Database */

2013-11-12T05:44:21Z

‎Model Organism Database

Lena: /* Model Organism Database */

2013-11-11T06:44:07Z

‎Model Organism Database

Lena: /* Model Organism Database */

2013-11-11T06:32:02Z

‎Model Organism Database

Lena: /* Model Organism Database */

2013-11-11T06:31:05Z

‎Model Organism Database

Lena: /* Model Organism Database */

2013-11-11T06:08:18Z

‎Model Organism Database

Lena: /* Methods */

2013-11-11T02:02:22Z

‎Methods

Lena: /* Genome Structure and Content */

2013-11-11T01:59:34Z

‎Genome Structure and Content

Lena: /* Results and Discussions */

2013-11-11T01:56:14Z

‎Results and Discussions

← Older revision		Revision as of 17:46, 14 November 2013
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	*The interface is not very user-friendly. There is no help section or tutorial. If you know exactly what you are searching for, there are links to click on, but if you are just browsing it is not inviting. The sample query seemed to make sense.		*The interface is not very user-friendly. There is no help section or tutorial. If you know exactly what you are searching for, there are links to click on, but if you are just browsing it is not inviting. The sample query seemed to make sense.
	*The gene format is for Leishmania major LmjF.##.####		*The gene format is for Leishmania major LmjF.##.####
		+
		+	[[Category: Leishmania Major]]

@@ Line 99: / Line 99: @@
 ==Model Organism Database==
 Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61
-*The Database provides links to identify genes, identify genomic sequences, and identify isolates.  It is a meta-database and is curated electronically.
+*The Database provides links to identify genes, identify genomic sequences, and identify isolates.  It is a meta-database and is curated manually by a community.
 *The database in maintained by the EuPathDP Scientific working group with Scientific advisors for Leishmania: Richard Burchmore  from University of Glasgow, Barbara Papadopoulou from Laval University, Jeremy Mottram from University of Glasgow, and Angela Cruz from Universidade de São Paulo.
 *They are funded by the Bill and Melinda Gates Foundation and by the Wellcome Trust.

@@ Line 104: / Line 104: @@
 *There are no access restrictions to the database.  It is open to the public as long as they cite the database.
 *The database is updated as new research arises, but not on a regular basis.  It was last updated on September 25th, 2013.
-*There are links to
+*There are links to GeneDB.

@@ Line 100: / Line 100: @@
 Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61
 *The Database provides links to identify genes, identify genomic sequences, and identify isolates.  It is a meta-database and is curated electronically.
-*The database in maintained by the EuPathDP Scientific working group with Scientific advisors for Leishmania: Richard Burchmore (University of Glasgow, United Kingdom)
+*The database in maintained by the EuPathDP Scientific working group with Scientific advisors for Leishmania: Richard Burchmore  from University of Glasgow, Barbara Papadopoulou from Laval University, Jeremy Mottram from University of Glasgow, and Angela Cruz from Universidade de São Paulo.
-Barbara Papadopoulou (Laval University, Canada)
-Jeremy Mottram (University of Glasgow, United Kingdom)
-Angela Cruz (Universidade de São Paulo, Brazil)
 *They are funded by the Bill and Melinda Gates Foundation and by the Wellcome Trust.
 *There are no access restrictions to the database.  It is open to the public as long as they cite the database.
 *The database is updated as new research arises, but not on a regular basis.  It was last updated on September 25th, 2013.
 *There are links to

← Older revision		Revision as of 06:31, 11 November 2013
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	==Model Organism Database==		==Model Organism Database==
	Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61		Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61
		+	*The Database provides links to identify genes, identify genomic sequences, and identify isolates. It is a meta-database and is curated electronically.
		+	*The database in maintained by the EuPathDP Scientific working group with Scientific advisors for Leishmania: Richard Burchmore (University of Glasgow, United Kingdom)
		+	Barbara Papadopoulou (Laval University, Canada)
		+	Jeremy Mottram (University of Glasgow, United Kingdom)
		+	Angela Cruz (Universidade de São Paulo, Brazil)
		+	*They are funded by the Bill and Melinda Gates Foundation and by the Wellcome Trust.
		+	*There are no access restrictions to the database. It is open to the public as long as they cite the database.
		+	*The database is updated as new research arises, but not on a regular basis. It was last updated on September 25th, 2013.
		+	*There are links to

← Older revision		Revision as of 06:08, 11 November 2013
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	==Model Organism Database==		==Model Organism Database==
		+	Database: http://tritrypdb.org/tritrypdb/getDataset.do?question=GeneQuestions.GenesByTaxon&display=detail#61

@@ Line 50: / Line 50: @@
 ===Methods===
-The researchers used shot-gun sequencing.  Shot gun sequencing breaks up DNA into many fragments, then sequences them into what are called ''reads''.  A researcher would perform this several times to get many reads, then a computer uses the overlapping ends of reads to generate a full and continuous sequence.  In this project, large-insert clones and purified chromosomal DNA were shotgun sequenced.  This allowed them to generate a full sequence for each of ''Leishmania's'' 36 chromosomes.  The sequences were then compared to an optical map to ensure accuracy.  Additionally, the ''Leishmania'' genome was analysis with the help of algorithms to predict numbers of RNA genes, pseudogenes, and protein-coding genes.
+The researchers used shot-gun sequencing.  Shot gun sequencing breaks up DNA into many fragments, then sequences them into what are called ''reads''.  A researcher would perform this several times to get many reads, then a computer uses the overlapping ends of reads to generate a full and continuous sequence.  In this project, large-insert clones and purified chromosomal DNA were shotgun sequenced.  This allowed them to generate a full sequence for each of ''Leishmania's'' 36 chromosomes.  The genome sequence was determined on a chromosome-by-chromosome basis.  The sequences were then compared to an optical map to ensure accuracy.  Additionally, the ''Leishmania'' genome was analysis with the help of algorithms to predict numbers of RNA genes, pseudogenes, and protein-coding genes.
 ===Results and Discussions===

@@ Line 66: / Line 66: @@
 **74 groups are orthologous for ''L. major:'' and ''T. brucei.''
 **482 groups are orthologous for ''L. major'' and ''T. cruzi.''
 ====RNA Processing====
 *Regulation of splicing probably appeared early in eukaryotic evolution.

@@ Line 60: / Line 60: @@
 :Below is Table 1 from the paper, which summarized the ''Leishmania'' genome.
 :[[File:Leishmania table1.png]]
 *The ends of each ''Leishmania major'' chromosome contain a previously reported tripartite "repeated-repeat" structure.