Bacterial Polysaccharide Gene Database (BPGD) Help


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This page contains information about the Bacterial Polysaccharide Gene Database (BPGD), and help for querying the database through the World Wide Web. The information was last updated on 10th February 1998. 

 

 

 

 

 

 

 

 


The Bacterial Polysaccharide Gene Database

Introduction and History

The Bacterial Polysaccharide Gene Database (BPGD) is a computer database of information about bacterial polysaccharide genes. The idea for a database was prompted by a desire to promote the recommendations for a new bacterial polysaccharide gene nomenclature, the BPGN (see below). A particular aim was to make it easy for researchers to look up an alternate name for a gene. We are also trying to link the genes and their products to other information (GenBank entries, EC numbers, polysaccharide structures, Medline references) and hope that the database may become generally useful to research groups interested in bacterial polysaccharide molecular biology.

Initially the database and browsing/querying software was developed with Microsoft FoxPro software and distributed as stand alone executable files which ran on both Macintosh and Windows platforms. As of February 1998 we abandoned this system. The current (and much improved) version of the database is implemented in Filemaker Pro 4.0 software (Claris Corp.) which allows querying through the World Wide Web.

BPG Nomenclature

The BPGD uses BPG nomenclature (BPGN, or NewNom) for names of genes involved in the production of polymorphic repeat unit surface polysaccharides such as O-antigens and capsules. This is a system recently developed for naming newly described polysaccharide genes, and for renaming previously studied genes (with old names such as rfa, rfb and cps).

Description

The BPGD is a relational database which contains information about genes involved in the synthesis of bacterial repeat unit surface polysaccharides. Several assumptions about gene organisation and function are built in to the structure of the database - not all are universally correct but were adopted during design of the database for the sake of expediency. The assumptions are:

Scope

When first established the BPGD contained only genes described by those who had contributed to the development of the BPGN system and applied BPGN names to their genes. (To make it more useful, the database has been expanded to include other sets of genes, whether or not the BPGN system has been adopted by the author).

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Querying the Database through the World Wide Web

Overview

There are two modes of querying - one for getting information about a cluster of genes, and the other for getting information about a particular gene. In both cases you fill out specifications for your query and then get a hit list of active links that you can follow to get detailed information about a specific cluster or gene record.

Searching for information about a cluster of genes

The fields available for querying are:

Gene cluster:

The exact name of the gene cluster record, chosen from a list of valid names.

Reference:

Part of a bibliographic reference cited in the gene cluster record (e.g. an author's name; a word in the title)

Polysaccharide class:

A class of polysaccharide (e.g. extracellular polysaccharide slime; O-antigen), chosen from a list of valid names.

Specificity:

Part of the description of the specificity, serological type, or other characteristic of the polysaccharide (e.g. O16; colanic acid)

Species:

The exact name of the species which is the biological source of the gene cluster, chosen from a list of valid names.

Subspecies/strain:

Part of the description of the other details pertaining to the biological source of the gene cluster (e.g. K-12).

GenBank accession number:

The exact name of an accession number specifying a GenBank DNA sequence associated with the gene cluster - this is a number (e.g. L39794).

Gene product:

Part of the description of the function of the product of one of the genes within the cluster (e.g. transferase)

BPGN gene name:

The BPGN name of a gene within the cluster. The query need only match the beginning of the name (e.g. the query rml will find gene names rmlA, rmlB, rmlC, etc.)

Old gene name:

Other (non-BPGN, usually outmoded) names of a gene within the cluster. The query need only match the beginning of the name (e.g. the query rfb will find gene names rfbA, rfbB, rfbC, etc.)

Created (MM/DD/YY):

The date the gene cluster record was created, where MM is a month, DD is a date, and YY is a year (e.g. 2/10/98 is February 10th 1998). The operator can be set to specify exactly a particular date, before a particular date, up to and including a particular date, on or since a particular date, or after a particular date.

Last updated (MM/DD/YY):

The date information in the gene cluster record was last updated. The operator can be set to specify exactly a particular date, before a particular date, up to and including a particular date, on or since a particular date, or after a particular date.

 

Searching for information about a particular gene

The fields available for querying are:

BPGN gene name:

The BPGN name of the gene. The query need only match the beginning of the name (e.g. the query rml will find gene names rmlA, rmlB, rmlC, etc.)

Old gene name:

Other (non-BPGN, usually outmoded) names of the gene. The query need only match the beginning of the name (e.g. the query rfb will find gene names rfbA, rfbB, rfbC, etc.)

NCBI protein sequence identifier:

The exact name of an NCBI sequence identifier specifying a protein sequence associated with the gene product - this is a number (e.g. ####).

Gene cluster:

The exact name of the gene cluster record, chosen from a list of valid names.

Product:

Part of the description of the name of the product of the gene (e.g. transferase).

Product class:

A class of gene product (e.g. glycosyl transferase; O-antigen polymerase), chosen from a list of valid names.

Product function:

Part of the description of the function of the product of the gene (e.g. Glc-1-P ).

EC number:

Part of the enzyme commission number assigned to the product of the gene (e.g. EC 2.7.7.24; or 2.7.7)

Last updated (MM/DD/YY):

The date information in the gene record was last updated. The operator can be set to specify exactly a particular date, before a particular date, up to and including a particular date, on or since a particular date, or after a particular date.

Created (MM/DD/YY):

The date the gene record was created, where MM is a month, DD is a date, and YY is a year (e.g. 2/10/98 is February 10th 1998). The operator can be set to specify exactly a particular date, before a particular date, up to and including a particular date, on or since a particular date, or after a particular date.

 

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Bugs and limitations

When a link is followed from a gene back to a gene cluster the references are not displayed. This is not the case if the same gene cluster is found by searching from the gene cluster search page. This was fixed 20.09.02.

 

Although links to the Complex Carbohydrate Structural Database (CarbBank) are working in most instances the CCSD structural identifier has not yet been added.

References are not being updated regularly and users are encouraged to follow links to the National Center for Biotechnology Information's Entez system to look for recent publications and for material related to references in the BPGD.

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BPGD Data Submissions

We would like to add as many relevent genes and gene clusters as possible to the BPGD database. We are at present in general only adding data for genes where the major authors concerned are accepting the BPGN system of nomenclature. To help us in this we have a submission form which you can download

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Acknowledgements and Copyright

The BPG database and the BPGD browser were developed by Matthew Hobbs and Peter Reeves at the Department of Microbiology (now part of the School of Molecular and Microbial Biosciences), University of Sydney, Australia.

The University of Sydney hereby reserves Copyright© 1998

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For more information

 

For further information about the BPGD or the Web query system contact:

Prof. Peter Reeves

Discipline of Microbiology (G08)

School of Molecular and Microbial Biosciences

University of Sydney, NSW 2006

Australia

Phone: +612 9351 6048

Fax: +612 9351 4571

reeves@angis.usyd.edu.au

 

 

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