Dataset: Tam genome analysis

Name: Thermovibrio ammonificans HB1 genome manual curation
Published: 2020-04-13
Keywords: oceans

DOI:10.26008/1912/bco-dmo.809272.1

Project:

Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere (Deep Biosphere Energy Limitation)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Principal Investigator:

Donato Giovannelli (Rutgers University)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-04-13

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Thermovibrio ammonificans HB1 genome manual curation

Abstract:

Thermovibrio ammonificans HB1 genome manual curation. Methods are further described in Giovannelli et al. (2012).

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-04-13	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.809272.1	2022-03-18

Description

Thermovibrio ammonificans HB1 genome manual curation. Methods are further described in Giovannelli et al. (2012).

Data Processing Description

Manual curation of the genome was performed using blastn and blastp against the non-redundant database, the conserved domain database, the Kyoto Encyclopedia of Genes and Genomes, and the PFAM database. Coding sequence similarities were compared using translated protein sequence. Metabolic pathways were reconstructed on the basis of available genomic, physiologic, and biochemical information and using Kyoto Encyclopedia of Genes and Genomes and SEED pathways as template.

Plots generated using this dataset can be found at:
http://genomevolution.org/r/9vb3
http://genomevolution.org/r/9vb4
http://genomevolution.org/r/9vb8

Data Files

File
tam_genome.csv (Comma Separated Values (.csv), 833.15 KB) MD5:39f20860ff9745d30cd629cabb919bbe Primary data file for dataset ID 809272

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0939564

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Organism	taxid of the organism	unitless	taxon
Chromosome	chromosome where the gene is located	unitless	no_bcodmo_term
Contig	chromosome where the gene is located	unitless	no_bcodmo_term
Gene	locus name for the gene	unitless	no_bcodmo_term
Strand	DNA strand where the gene is	unitless	no_bcodmo_term
Start	start position in base pairs	unitless	no_bcodmo_term
Stop	stop position in base pairs	unitless	no_bcodmo_term
Called_By	gene prediction by	unitless	no_bcodmo_term
Product	gene function name	unitless	no_bcodmo_term
Product_From	product called by which database	unitless	no_bcodmo_term
Color	product called by which database	unitless	no_bcodmo_term
Accession	accession number of the match from blastp	unitless	accession_number
Organism_Name	name of the organism	unitless	taxon
Positivities	% of positivities in the sequence alignment	unitless	no_bcodmo_term
Identities	% of identities in the sequence alignment	unitless	no_bcodmo_term
NR	function assigned by NCBI NR database	unitless	no_bcodmo_term
SPTR	function assigned by SPTR	unitless	no_bcodmo_term
PFAM	function assigned by PFAM	unitless	no_bcodmo_term
TIGRFAM	function assigned by TIGRFAM	unitless	no_bcodmo_term
KEGG	function assigned by KEGG	unitless	no_bcodmo_term
COGs	COG function assigned	unitless	no_bcodmo_term

Status message

Database

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Dataset: Tam genome analysis