Cbcb:Pop-Lab:Chris-Report - Revision history

Cmhill: /* Tasks */

2009-06-13T00:47:18Z

Tasks

← Older revision		Revision as of 00:47, 13 June 2009
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	*Investigated GO annotation tools that Bo has linked me to.		*Investigated GO annotation tools that Bo has linked me to.
	*I have been working on the Snail, ''Lottia gigantea'', genome.		*I have been working on the Snail, ''Lottia gigantea'', genome.
	*Found the top 10% intergenic space with relative ~~easy~~, however there was no GO annotation file for the genes.		*Found the top 10% intergenic space with relative ease, however there was no GO annotation file for the genes. Most of the genomes of interest will not have a GO annotation file (shocker, I know).
	*BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/		*BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/
	*Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.		*Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.

Cmhill: /* Tasks */

2009-06-13T00:45:46Z

Tasks

← Older revision		Revision as of 00:45, 13 June 2009
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	===Tasks===		===Tasks===
	'''Intergenic space and gene ontology work'''		'''Intergenic space and gene ontology work'''
			*Investigated GO annotation tools that Bo has linked me to.
	*I have been working on the Snail, ''Lottia gigantea'', genome.		*I have been working on the Snail, ''Lottia gigantea'', genome.
	*Found the top 10% intergenic space. BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/		*Found the top 10% intergenic space with relative easy, however there was no GO annotation file for the genes.
	*BLAST took around 12 hours for ~2200 sequences.		*BLAST'd the sequences using Blast2GO, '''ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.''' http://www.blast2go.org/
			*Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.
			*BLAST took around 8 hours for ~2200 sequences using an online database. I will run another group on the CBCB's BLAST.
	*GO annotation using Blast2GO took around 24 hours.		*GO annotation using Blast2GO took around 24 hours.
	*I plan on running HMMs for the approximate 200 sequences with no suitable hits this weekend.		*I plan on running HMMs for the approximate 200 sequences with no suitable hits this weekend.
	'''Partition'''		'''Partition'''
	*Drastically overhauling the backend of my partition program to make it more extendable/robust.		*Drastically overhauling the backend of my partition program to make it more extendable/robust.
	*Adding XML support to make parsing easier.		*Adding XML support to make parsing easier and increase possible functionality.
			*Need to focus on getting James something usable asap.

	===Summer Goals===		===Summer Goals===
	*Finish analyzing the intergenic space of the incomplete genomes. Determine future possibilities/publications.		*Finish analyzing the intergenic space of the incomplete genomes. Determine future possibilities/publications.

Cmhill at 00:36, 13 June 2009

2009-06-13T00:36:44Z

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 == June 12, 2009 ==
 ===Summer Goals===
 == Mar 2, 2009 ==

Cmhill: /* Mar 2, 2009 */

2009-06-12T17:52:47Z

Mar 2, 2009

← Older revision		Revision as of 17:52, 12 June 2009
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			== June 12, 2009 ==
			===Summer Goals===

	== Mar 2, 2009 ==		== Mar 2, 2009 ==
	===Tasks===		===Tasks===

Cmhill at 02:27, 2 March 2009

2009-03-02T02:27:26Z

← Older revision		Revision as of 02:27, 2 March 2009
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	*Update elements based on Adam's changes to Insignia.		*Update elements based on Adam's changes to Insignia.
	*Find something to write about.		*Find something to write about.
			===Interesting Stuff===
	http://med.stanford.edu/news_releases/2008/july/aging-worm.html		*New insights into aging based on transcription factors, [http://med.stanford.edu/news_releases/2008/july/aging-worm.html Prevailing theory of aging challenged in Stanford worm study]

Cmhill at 02:25, 2 March 2009

2009-03-02T02:25:43Z

← Older revision		Revision as of 02:25, 2 March 2009
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	== Mar 2, 2009 ==		== Mar 2, 2009 ==
			===Tasks===
	'''Intergenic space and gene ontology work with Cristian'''		'''Intergenic space and gene ontology work with Cristian'''
	*Approach		*Approach
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	*Update elements based on Adam's changes to Insignia.		*Update elements based on Adam's changes to Insignia.
	*Find something to write about.		*Find something to write about.

			http://med.stanford.edu/news_releases/2008/july/aging-worm.html

Cmhill at 02:23, 2 March 2009

2009-03-02T02:23:10Z

← Older revision		Revision as of 02:23, 2 March 2009
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	**Waterflea, ''Daphnia pulex''		**Waterflea, ''Daphnia pulex''
	*Incomplete genomes that require blast		*Incomplete genomes that require blast
	**Gastropod Snail, Lottia gigantea		**Gastropod Snail, ''Lottia gigantea''
	**Polychaete Worm, Capitella sp		**Polychaete Worm, ''Capitella sp''
	*Future genomes		*Future genomes
	**Leech, ''Helobdella robusta''		**Leech, ''Helobdella robusta''
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	**Sea Slug,'' Aplysia californica''		**Sea Slug,'' Aplysia californica''
	**Snail,'' Biomphalaria glabrata''		**Snail,'' Biomphalaria glabrata''
	**Slime-mold, Dictyostelium purpureum QSDP1		**Slime-mold, ''Dictyostelium purpureum QSDP1''
	*Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.		*Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.

Cmhill at 02:22, 2 March 2009

2009-03-02T02:22:32Z

← Older revision		Revision as of 02:22, 2 March 2009
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	== Mar 2, 2009 ==		== Mar 2, 2009 ==
	'''Intergenic ~~Space~~ and ~~Gene Ontology~~ work with Cristian'''		'''Intergenic space and gene ontology work with Cristian'''
	*Approach		*Approach
	*Get the gene-spacing information - typically a simple parse of GFF files, if they are available.		Get the gene-spacing information - typically a simple parse of GFF files, if they are available.
	*Get the gene function information - use GO if available.		Get the gene function information - use GO if available.
	*Rank the genes based on 5' spacing size.		Rank the genes based on 5' spacing size.
	*Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge		Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge
	*Completed genomes		*Completed genomes
	**Anenome, ''Nematostella vectensis''		**Anenome, ''Nematostella vectensis''
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	**Sea Slug,'' Aplysia californica''		**Sea Slug,'' Aplysia californica''
	**Snail,'' Biomphalaria glabrata''		**Snail,'' Biomphalaria glabrata''
			**Slime-mold, Dictyostelium purpureum QSDP1
			*Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.

			'''Partitioning System'''
			*Splitting contigs based on "subgroup" information - essentially extending breaking up an entire assembly into multiple "sub-assemblies" each containing just reads from a single subgroup.

			'''Conserved genomic elements in bacteria'''
			*Update elements based on Adam's changes to Insignia.
			*Find something to write about.

Cmhill at 02:10, 2 March 2009

2009-03-02T02:10:17Z

← Older revision		Revision as of 02:10, 2 March 2009
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	~~Test~~.		== Mar 2, 2009 ==
			'''Intergenic Space and Gene Ontology work with Cristian'''
			*Approach
			*Get the gene-spacing information - typically a simple parse of GFF files, if they are available.
			*Get the gene function information - use GO if available.
			*Rank the genes based on 5' spacing size.
			*Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge
			*Completed genomes
			**Anenome, ''Nematostella vectensis''
			**Frog, ''Xenopus tropicalis''
			**Waterflea, ''Daphnia pulex''
			*Incomplete genomes that require blast
			**Gastropod Snail, Lottia gigantea
			**Polychaete Worm, Capitella sp
			*Future genomes
			**Leech, ''Helobdella robusta''
			**Flatworm (Planaria), '' Schmidtea mediterranea''
			**Sea Slug,'' Aplysia californica''
			**Snail,'' Biomphalaria glabrata''

Cmhill at 23:38, 11 February 2009

2009-02-11T23:38:30Z

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