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Bacterial protein tYrosine Kinase database

Abbreviation:BYKdb

General Information

The Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.

Homepage http://bykdb.ibcp.fr

Countries that developed this resource France

Created in 2011

Taxonomic range

Bacteria

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: BYKdb; Bacterial protein tYrosine Kinase database; DOI: https://doi.org/10.25504/FAIRsharing.jr30xc; Last edited: Feb. 12, 2019, 1:42 p.m.; Last accessed: Apr 07 2020 12:55 a.m.

Publication for citation BYKdb: the Bacterial protein tYrosine Kinase database. Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deleage G,Combet C; Nucleic Acids Res ; 2011; 10.1093/nar/gkr915;

Record updated: Feb. 12, 2019, 1:39 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.jr30xc' by 'The FAIRsharing Team' at 13:39, 12 Feb 2019 (approved):

	'organizations' has been modified:
		Before:
			PRABI  Rhone-Alpes Bioinformatics Center, France|http://www.prabi.fr|Funds
			The French National Research Agency (ANR), France|http://www.agence-nationale-recherche.fr|Funds
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains,Funds
			National Centre for Scientific Research (CNRS), Paris, France|http://www.cnrs.fr/index.php|Maintains
			Universite de Lyon, France|https://www.universite-lyon.fr/version-anglaise/udl-en-6709.kjsp|Maintains
			The French National Research Agency (ANR), France|http://www.agence-nationale-recherche.fr|Funds
		After:
			PRABI  Rhone-Alpes Bioinformatics Center, France|http://www.prabi.fr|Maintains,Funds
			The French National Research Agency (ANR), France|http://www.agence-nationale-recherche.fr|Funds
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains,Funds
			National Centre for Scientific Research (CNRS), Paris, France|http://www.cnrs.fr/index.php|Maintains
			Universite de Lyon, France|https://www.universite-lyon.fr/version-anglaise/udl-en-6709.kjsp|Maintains
			Centre de Recherche en Cancerologie de Lyon (CRCL), France|http://www.crcl.fr/|Maintains
		Added:
			PRABI  Rhone-Alpes Bioinformatics Center, France|http://www.prabi.fr|Maintains,Funds
			Centre de Recherche en Cancerologie de Lyon (CRCL), France|http://www.crcl.fr/|Maintains
		Removed:
			PRABI  Rhone-Alpes Bioinformatics Center, France|http://www.prabi.fr|Funds

	'standardsImplemented' has been modified:
		Before:
			CLUSTAL-W Alignment Format
			UniProtKB XML Format
			CLUSTAL-W Dendrogram Guide File Format
			FASTA Sequence Format
		After:
			CLUSTAL-W Alignment Format
			UniProtKB XML Format
			FASTA Sequence Format
		Added:
		Removed:
			CLUSTAL-W Dendrogram Guide File Format

	'supportLinks' has been modified:
		Before:
			help|https://bykdb.ibcp.fr/BYKdb/BYKdbHelp
		After:
			contact form|https://bykdb.ibcp.fr/BYKdb/BYKdbContact
			help|https://bykdb.ibcp.fr/BYKdb/BYKdbHelp
			online documentation|https://bykdb.ibcp.fr/BYKdb/BYKdbStats
			online documentation|https://bykdb.ibcp.fr/BYKdb/BYKdbNews
		Added:
			contact form|https://bykdb.ibcp.fr/BYKdb/BYKdbContact
			online documentation|https://bykdb.ibcp.fr/BYKdb/BYKdbStats
			online documentation|https://bykdb.ibcp.fr/BYKdb/BYKdbNews
		Removed:

	'onto_domains' has been modified:
		Before:
			Protein sequence
		After:
			Protein sequence
			Protein structure
			Structure
			molecular_function
		Added:
			Protein structure
			Structure
			molecular_function
		Removed:

	'dataProcesses' has been modified:
		Before:
			access to historical files available upon request
			no versioning policy
			automated annotation
			monthly release
			SQL database dump
			file download(txt)
			web interface
		After:
			Browse Precomputed Datasets
			Browse Annotated Sequences
		Added:
			Browse Precomputed Datasets
			Browse Annotated Sequences
		Removed:
			access to historical files available upon request
			no versioning policy
			automated annotation
			monthly release
			SQL database dump
			file download(txt)
			web interface

	'publications' has been modified:
		Before:
			Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase.|Grangeasse C., Doublet P., Vaganay E., Vincent C., Delage G., Duclos B., Cozzone AJ., |Gene|1997
			Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.|Jadeau F., Bechet E., Cozzone AJ., Delage G., Grangeasse C., Combet C., |Bioinformatics|2008
			Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.|Bechet E., Guiral S., Torres S., Mijakovic I., Cozzone AJ., Grangeasse C., |Amino Acids|2009
		After:
			Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase.|Grangeasse C., Doublet P., Vaganay E., Vincent C., Delage G., Duclos B., Cozzone AJ., |Gene|1997
			Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.|Jadeau F., Bechet E., Cozzone AJ., Delage G., Grangeasse C., Combet C., |Bioinformatics|2008
			Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.|Bechet E., Guiral S., Torres S., Mijakovic I., Cozzone AJ., Grangeasse C., |Amino Acids|2009
			BYKdb: the Bacterial protein tYrosine Kinase database.|Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deleage G,Combet C|Nucleic Acids Res|2011
		Added:
			BYKdb: the Bacterial protein tYrosine Kinase database.|Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deleage G,Combet C|Nucleic Acids Res|2011
		Removed:

	'tools' has been modified:
		Before:
			BlastP||https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_blast.html
			ClustalW||https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_clustalw.html
		After:
			BlastP||https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_blast.html
			ClustalW||https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_clustalw.html
			Annotate||https://bykdb.ibcp.fr/BYKdb/BYKdbAnnotate
		Added:
			Annotate||https://bykdb.ibcp.fr/BYKdb/BYKdbAnnotate
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.jr30xc' by 'The FAIRsharing Team' at 09:51, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
		After:
			Amino acid sequence
			Life Science
		Added:
			Amino acid sequence
			Life Science
		Removed:

	'organizations' has been modified:
		Before:
			The French National Research Agency (ANR), France|http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/|Funds
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains
			National Centre for Scientific Research (CNRS), Paris, France|http://www.cnrs.fr/index.php|Maintains
			PRABI  Rhone-Alpes Bioinformatics Center|http://www.prabi.fr|Funds
			The French National Research Agency|http://www.agence-nationale-recherche.fr|Funds
			Universite de Lyon|https://www.universite-lyon.fr/version-anglaise/udl-en-6709.kjsp|Maintains
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Funds
		After:
			The French National Research Agency (ANR), France|http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/|Funds
			PRABI  Rhone-Alpes Bioinformatics Center|http://www.prabi.fr|Funds
			The French National Research Agency|http://www.agence-nationale-recherche.fr|Funds
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains,Funds
			National Centre for Scientific Research (CNRS), Paris, France|http://www.cnrs.fr/index.php|Maintains
			Universite de Lyon|https://www.universite-lyon.fr/version-anglaise/udl-en-6709.kjsp|Maintains
		Added:
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains,Funds
		Removed:
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Funds

Edits to 'https://fairsharing.org/FAIRsharing.jr30xc' by 'The FAIRsharing Team' at 13:47, 02 Sep 2016 (approved):

	'name' has been modified:
		Before: BYKdb: The Bacterial protein tYrosine Kinase database
		After: Bacterial protein tYrosine Kinase database

Edits to 'https://fairsharing.org/FAIRsharing.jr30xc' by 'The FAIRsharing Team' at 21:30, 31 Aug 2016 (approved):

	'description' has been modified:
		Before: Bacterial protein tYrosine Kinase database
		After: Bacterial protein tYrosine Kinase database (BYKdb) contains computer-annotated BY-kinase sequences. The database web interface allows static and dynamic queries and provides integrated analysis tools including sequence annotation.

Support

General

contact form	Contact Form
help	Help Pages
online documentation	Statistics
online documentation	News

Tools

BlastP	https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_bl ...
ClustalW	https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?&page=/NPSA/npsa_cl ...
Annotate	https://bykdb.ibcp.fr/BYKdb/BYKdbAnnotate

Access / Retrieve Data

Conditions of Use

Data Access

Browse Precomputed Datasets	https://bykdb.ibcp.fr/BYKdb/BYKdbDataset
Browse Annotated Sequences	https://bykdb.ibcp.fr/data/html/annotated/bykdb2html.html

Publications

Characterization of a bacterial gene encoding an autophosphorylating protein tyrosine kinase.

Grangeasse C., Doublet P., Vaganay E., Vincent C., Deléage G., Duclos B., Cozzone AJ.,
Gene 1997

View Paper (PubMed)

Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.

Jadeau F., Bechet E., Cozzone AJ., Deléage G., Grangeasse C., Combet C.,
Bioinformatics 2008

View Paper (PubMed)

Tyrosine-kinases in bacteria: from a matter of controversy to the status of key regulatory enzymes.

Bechet E., Guiral S., Torres S., Mijakovic I., Cozzone AJ., Grangeasse C.,
Amino Acids 2009

View Paper (PubMed)

BYKdb: the Bacterial protein tYrosine Kinase database.

Jadeau F,Grangeasse C,Shi L,Mijakovic I,Deleage G,Combet C
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

PRABI Rhone-Alpes Bioinformatics Center, France (Research institute) Lead
The French National Research Agency (ANR), France (Government body)
Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France (Government body)

Maintains

PRABI Rhone-Alpes Bioinformatics Center, France (Research institute) Lead
Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France (Government body)
National Centre for Scientific Research (CNRS), Paris, France (Government body)
Universite de Lyon, France (University)
Centre de Recherche en Cancerologie de Lyon (CRCL), France (Research institute) Lead

Grant Number(s)

ANR-07-JCJC0125-01 BACTYRKIN (The French National Research Agency (ANR), France)
GIS IBiSA (PRABI Rhone-Alpes Bioinformatics Center, France)

Bacterial protein tYrosine Kinase database

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