NCBI submission - Revision history

Dpuiu: /* Annotation */

2011-08-01T14:25:30Z

Annotation

← Older revision		Revision as of 14:25, 1 August 2011
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	ABC_r1112 for ribosomal RNA genes		ABC_r1112 for ribosomal RNA genes
	ABC_t1113 for tRNA genes		ABC_t1113 for tRNA genes

			* [http://www.ncbi.nlm.nih.gov/genomes/frameshifts/frameshifts.cgi frameshifts]

	* Generating the .tbl format from a TAB delinited format		* Generating the .tbl format from a TAB delinited format

2011-08-01T14:06:12Z

Annotation

← Older revision		Revision as of 14:06, 1 August 2011
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	=== Annotation ===		=== Annotation ===

			* Locus tag examples:
			ABC_I00001 for gene 1, chromosome I
			ABC_II00001 for gene 1, chromosome II
			ABC_r1112 for ribosomal RNA genes
			ABC_t1113 for tRNA genes

	* Generating the .tbl format from a TAB delinited format		* Generating the .tbl format from a TAB delinited format

2011-08-01T14:04:02Z

Links

← Older revision		Revision as of 14:04, 1 August 2011
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	* [http://www.ncbi.nlm.nih.gov/genome/assembly/agp/AGP_Specification.shtml AGP format]		* [http://www.ncbi.nlm.nih.gov/genome/assembly/agp/AGP_Specification.shtml AGP format]
	* [http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit.html Bacterial Genomes]		* [http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit.html Bacterial Genomes]
	* [http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit_annotation.html Annotation] [http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html Annotation Info] ,[http://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf Locus tag extra info]		* [http://www.ncbi.nlm.nih.gov/Genbank/genomesubmit_annotation.html Annotation]
			* [http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html Annotation Info]
			* [http://www.ncbi.nlm.nih.gov/genomes/locustag/Proposal.pdf Locus tag extra info]

	== Registration ==		== Registration ==

2011-05-23T15:16:09Z

dbGSS

← Older revision		Revision as of 15:16, 23 May 2011
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	OTHER_GSS: GSS00093, GSS000101		OTHER_GSS: GSS00093, GSS000101
	CITATION: #required		CITATION: #required
	Genomic sequences from Human		Genomic sequences from Human brain tissue
	brain tissue
	SEQ_PRIMER: M13 Forward		SEQ_PRIMER: M13 Forward
	P_END: 5'		P_END: 5'

2011-05-23T14:24:20Z

dbGSS

← Older revision		Revision as of 14:24, 23 May 2011
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	MEDUID: 92347897		MEDUID: 92347897
	TITLE: #required		TITLE: #required
	Genomic sequences from a subtracted retinal pigment epithelium		Genomic sequences from a subtracted retinal pigment epithelium library
	library
	AUTHORS: #required		AUTHORS: #required
	Gieser,L.; Swaroop,A.		Gieser,L.; Swaroop,A.

2011-05-20T16:53:37Z

dbGSS

← Older revision		Revision as of 16:53, 20 May 2011
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	= dbGSS =		= dbGSS =
	* 4 files:
			* 4 files: email to batch-sub@ncbi.nlm.nih.gov

	1. Publication		1. Publication
	TYPE: Pub #required		TYPE: Pub #required
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	4. GSS sequence file		4. GSS sequence file

	TYPE: GSS		TYPE: GSS #required
	STATUS: New		STATUS: New #required
	CONT_NAME: Sikela JM		CONT_NAME: Sikela JM #required
	GSS#: Ayh00001		GSS#: Ayh00001 #required
	CLONE: HHC189		CLONE: HHC189
	SOURCE: ATCC		SOURCE: ATCC
	SOURCE_INHOST: 65128		SOURCE_INHOST: 65128
	OTHER_GSS: GSS00093, GSS000101		OTHER_GSS: GSS00093, GSS000101
	CITATION:		CITATION: #required
	Genomic sequences from Human		Genomic sequences from Human
	brain tissue		brain tissue
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	HIQUAL_STOP: 285		HIQUAL_STOP: 285
	DNA_TYPE: Genomic		DNA_TYPE: Genomic
	CLASS: shotgun		CLASS: shotgun #required
	LIBRARY: Hippocampus, Stratagene (cat. #936205)		LIBRARY: Hippocampus, Stratagene (cat. #936205) #required
	PUBLIC:		PUBLIC: #required
	PUT_ID: Actin, gamma, skeletal		PUT_ID: Actin, gamma, skeletal
	COMMENT:		COMMENT:
	SEQUENCE:		SEQUENCE:
	AATCAGCCTGCAAGCAAAAGATAGGAATATTCACCTACAGTGGGCACCTCCTTAAGAAGCTG		AATCAGCCTGCAAGCAAAAGATAGGAATATTCACCTACAGTGGGCACCTCCTTAAGAAGCTG #required
	...		...
	\|\|		\|\|

			* Matching strings:
			CONT_NAME of GSS file and NAME field of the Contact file
			LIBRARY field of GSS file and NAME field of the Library file
			CITATION field of GSS file and TITLE field of the Publication file

2011-05-20T16:49:06Z

← Older revision		Revision as of 16:49, 20 May 2011
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	$ cd assembly		$ cd assembly
	$ put *.tar.gz		$ put *.tar.gz

			= dbGSS =
			* 4 files:
			1. Publication
			TYPE: Pub #required
			MEDUID: 92347897
			TITLE: #required
			Genomic sequences from a subtracted retinal pigment epithelium
			library
			AUTHORS: #required
			Gieser,L.; Swaroop,A.
			JOURNAL: Genomics
			VOLUME: 13
			ISSUE: 2
			PAGES: 873-6
			YEAR: 1992 #required
			STATUS: 4 #required :1=unpublished, 2=submitted, 3=in press, 4=published
			\|\|

			2. Library
			TYPE: Lib #required
			NAME: Rat Lambda Zap Express Library
			ORGANISM: Rattus norvegicus
			STRAIN: Sprague-Dawley
			SEX: male
			STAGE: embryonic day 17 post-fertilization
			TISSUE: aorta
			CELL_TYPE: vascular smooth muscle
			DESCR:
			Put description here.
			\|\|

			3. Contact
			TYPE: Cont
			NAME: Sikela JM
			FAX: 303 270 7097
			TEL: 303 270
			EMAIL: tjs@tally.hsc.colorado.edu
			LAB: Department of Pharmacology
			INST: University of Colorado Health Sciences Center
			ADDR: Box C236, 4200 E. 9th Ave., Denver, CO 80262-0236, USA
			\|\|

			4. GSS sequence file

			TYPE: GSS
			STATUS: New
			CONT_NAME: Sikela JM
			GSS#: Ayh00001
			CLONE: HHC189
			SOURCE: ATCC
			SOURCE_INHOST: 65128
			OTHER_GSS: GSS00093, GSS000101
			CITATION:
			Genomic sequences from Human
			brain tissue
			SEQ_PRIMER: M13 Forward
			P_END: 5'
			HIQUAL_START: 1
			HIQUAL_STOP: 285
			DNA_TYPE: Genomic
			CLASS: shotgun
			LIBRARY: Hippocampus, Stratagene (cat. #936205)
			PUBLIC:
			PUT_ID: Actin, gamma, skeletal
			COMMENT:
			SEQUENCE:
			AATCAGCCTGCAAGCAAAAGATAGGAATATTCACCTACAGTGGGCACCTCCTTAAGAAGCTG
			...
			\|\|

2011-05-16T14:28:50Z

Registration

← Older revision		Revision as of 14:28, 16 May 2011
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	* genome project id (5 digit); use it in e-mail correspondence		* genome project id (5 digit); use it in e-mail correspondence
	* locus_tags (3+ letter/digit)		* locus_tags (3+ letter/digit)

			* [http://www.ncbi.nlm.nih.gov/genomes/lltp.cgi Locus tag database] to check if the chosen locus tag is available

	== Requirements ==		== Requirements ==

2011-05-03T14:52:10Z

SRA

← Older revision		Revision as of 14:52, 3 May 2011
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	/nfshomes/dpuiu/Archives/JCVI/bin/phred2xmlTrace.pl		/nfshomes/dpuiu/Archives/JCVI/bin/phred2xmlTrace.pl

	= SRA =		= Genbank & SRA =

	server: ftp-trace.ncbi.nlm.nih.gov		server: ftp-trace.ncbi.nlm.nih.gov
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	Directory (Short reads): short_read/		Directory (Short reads): short_read/
	Directory (Sanger reads): uploads/		Directory (Sanger reads): uploads/
	Directory (test): test/ (~~~30 reads~~)		Directory (test): test/ (Assembled sequences)

	[http://www.ncbi.nlm.nih.gov/Traces/field_matrix_current.xls Validation table]		[http://www.ncbi.nlm.nih.gov/Traces/field_matrix_current.xls Validation table]

2010-12-13T15:20:56Z

AGP

← Older revision		Revision as of 15:20, 13 December 2010
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	=== AGP ===		=== AGP ===

			* [http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml AGP_Specification.shtml]
	* Sequence gaps : "fragment yes"		* Sequence gaps : "fragment yes"
	* Scaffold gaps : "contig no"		* Scaffold gaps : "contig no"