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Pathema was one of the eight
bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...
resource centers funded by the
National Institute of Allergy and Infectious Diseases The National Institute of Allergy and Infectious Diseases (NIAID, ) is one of the 27 institutes and centers that make up the National Institutes of Health (NIH), an agency of the United States Department of Health and Human Services. NIAID's mis ...
(NIAID), a component of the
National Institute of Health The National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. It was founded in 1887 and is part of the United States Department of Health and Human Servic ...
(NIH), which is an agency of the
United States Department of Health and Human Services The United States Department of Health and Human Services (HHS) is a cabinet-level executive branch department of the US federal government created to protect the health of the US people and providing essential human services. Its motto is ...
. Pathema was funded for five years from 2004 through a contract to The
J. Craig Venter Institute The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Ge ...
, and is currently led by PI Granger Sutton. Pathema is the web resource for JCVI's NIAID-funded Bioinformatics Resource Center, and was one of eight such centers designed to support bio-defense and infectious disease research. The overarching goal of Pathema is to provide a core resource that will accelerated scientific progress towards understanding, detection, diagnosis and treatment of diseases caused by six clades of Category A-C pathogens (''
Bacillus anthracis ''Bacillus anthracis'' is a gram-positive and rod-shaped bacterium that causes anthrax, a deadly disease to livestock and, occasionally, to humans. It is the only permanent (obligate) pathogen within the genus ''Bacillus''. Its infection is a ty ...
'', ''
Clostridium botulinum ''Clostridium botulinum'' is a Gram-positive bacteria, gram-positive, Bacillus (shape), rod-shaped, Anaerobic organism, anaerobic, endospore, spore-forming, Motility, motile bacterium with the ability to produce botulinum toxin, which is a neurot ...
'', ''
Burkholderia mallei ''Burkholderia mallei'' is a Gram-negative, bipolar, aerobic bacterium, a human and animal pathogen of genus '' Burkholderia'' causing glanders; the Latin name of this disease (''malleus'') gave its name to the species causing it. It is closely ...
'', ''
Burkholderia pseudomallei ''Burkholderia pseudomallei'' (also known as ''Pseudomonas pseudomallei'') is a Gram-negative, bipolar, aerobic, motile rod-shaped bacterium. It is a soil-dwelling bacterium endemic in tropical and subtropical regions worldwide, particularly in ...
'', ''
Clostridium perfringens ''Clostridium perfringens'' (formerly known as ''C. welchii'', or ''Bacillus welchii'') is a Gram-positive, bacillus (rod-shaped), anaerobic, spore-forming pathogenic bacterium of the genus '' Clostridium''. ''C. perfringens'' is ever-present ...
'', and ''
Entamoeba histolytica ''Entamoeba histolytica'' is an anaerobic organism, anaerobic parasitic amoebozoan, part of the genus ''Entamoeba''. Predominantly infecting humans and other primates causing amoebiasis, ''E. histolytica'' is estimated to infect about 35-50 mil ...
'') involved in new and re-emerging infectious diseases. Pathema provides comprehensive curated datasets for the targeted pathogen clades, along with advanced bioinformatics capabilities geared specifically towards biodefense requirements, and the identification of potential targets for vaccine development, therapeutics and diagnostics.


Supported Pathema organisms


Pathema analysis tools

Pathema supports a suite of over 50 web-based single gene, whole-genome and multi-genome comparative tools to facilitate analyses of genomic sequence and annotation data of over 80 NIAID Category A-C prokaryotic pathogens. Tools available on the BRC resource are developed and customized to best meet the scientific needs of the pathogen research community based on feedback solicited through community outreach. Additionally, they are designed to facilitate scientific exploration in the areas of functional curation, pathogenicity, therapeutics, comparative analysis and functional genomics. While every tool has several applications, taken together they provides numerous opportunities for discovery and hypothesis generation. The suite of Pathema analysis tools include: *''Over 25 different search capabilities allow users to mine and retrieve data stored in the BRC comparative database.'' Search tools query genes, genomes, sequences or text, matching user-defined strings across gene loci, gene symbols and protein product names. Other queries include EC#, GenBank, SwissProt, and GO id searches. Common sequence search methods such as BLAST, HMM and protein motif searches are also available. *''Over 20 different displays and analyses of whole-genome data.'' Whole-genome data can be displayed graphically as a linear representation of genes on regions of a chromosome or as a complete circle for an entire chromosome. Users can investigate biochemical pathways, codon usage tables, percent GC plots, computer generated 2D and restriction digest gels, and retrieve summary information such as average gene size or numbers of coding regions as viewable and downloadable tables and lists. *''Over 15 different comparative analysis tools.'' The basis for Pathema's comparative tools is either pre-generated protein clusters or All vs. All searches. Incorporated, are the most popular tools of the publicly available Sybil comparative analysis suite. Sybil uses pre-generated protein clusters as the underlying data for its synteny gradient and comparative genomic displays, with protein cluster ortholog, paralog and singleton data available to the user. *''Individual gene pages highlighting annotation data and associated evidence as well as single gene analysis tools.'' Annotation data displayed and downloadable includes product name, gene symbol, EC number, GO ids, functional role category assignment, DNA sequence and protein sequence. Calculating the TmHMM profile, secondary structure and third position GC-Skew are just a few types of analyses users can perform. Links to other relevant resources such as Swiss-Prot, GenBank, Prosite, Pfam, etc., are also available.


References

* *{{cite journal , vauthors=Greene JM, Collins F, Lefkowitz EJ, etal , title=National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics , journal=Infection and Immunity , volume=75 , issue=7 , pages=3212–9 , date=July 2007 , pmid=17420237 , pmc=1932942 , doi=10.1128/IAI.00105-07


External links


Pathema PublicationsPathema PresentationsNIAID home page
The NIAID page describing the goals and activities of the BRCs
PathogenPortal
- A hub site for the BRCs; provides Summary information Bioinformatics organizations Biological databases