Three New Bioinformatics Tools Available

The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.

Microarray Suggestion Criteria

The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.

Home  > Microarray  > Available Microarrays

Available Microarrays

Organism

Design Strains

Current Versions

Older Versions

Actinobacillus actinomycetemcomitans

HK1651

Version 1

Aspergillus fumigatus

isolate Af293

Version 3

Version 1

Version 2

Aspergillus nidulans

FGSC A4

Version 2

Version 1

Bacillus anthracis

Ames

A2012

Version 3

Version 1

Version 2

Burkholderia mallei/pseudomallei

ATCC 23344 (mallei)

GB8 Horse 4 (mallei)

1710b (pseudomallei)

K96243 (pseudomallei)

Version 2

Version 1

Campylobacter jejuni

RM1221

81-176

269.97

NCTC 11168

plasmid pCJ1170 (strain RM1170)

Version1

Candida albicans

SC5314

Version 1

Chlamydia trachomatis/pneumoniae

D/UW-3/CX (serovar D)

AR39

CWL029

J138

Version 1

Version 2

Clostridium botulinum

Hall strain A

Version 1

Version 2

Corona Virus Array

Human Coronavirus strain 299E

SARS Coronavirus strain Tor2

Porcine epidemic diarrhea virus

Transmissible gastroenteritis virus

Bovine coronavirus

Murine hepatitis virus

Human coronavirus OC43

Avian infectious bronchitis virus

Version 1

Francisella tularensis

LVS

SCHU 4

pFNL10 (plasmid)

pOM1 (plasmid)

Version 2

Version 1

Fusobacterium nucleatum

ATCC 25586

ATCC 10953

Version 2

Giardia lamblia

WB strain, clone C6

Version 2

Version 1

Haemophilus influenzae

Rd KW20

86-028NP

R2846

R2866

pF3031 (biotype aegyptius)

pF3028 (biotype aegyptius)

F3031 genetic island (biotype aegyptius)

HK1212 (Gene discovery)

Version 2

Version 1

Helicobacter pylori

26695

J99

Version 1

Version 2

Listeria monocytogenes

EGD-e

1/2a F6854

4b F2365

4b H7858

Version 3

Version 1

Version 2

Mycobacterium smegmatis

MC2 155

Version 4

Version 1

Version 2

Version 3

Mycobacterium tuberculosis

H37Rv

CDC1551

Version 4

Version 1

Version 2

Version 3

Neisseria gonorrhoeae/meningitidis

FA1090

Z2491 (serogroup A)

MC58 (serogroup B)

Version 3

Version 1

Version 2

Plasmodium falciparum

3D7

Version 3

Version 1

Version 2

Plasmodium vivax

Sal-1

Version 1

Porphyromonas gingivalis

W83

Version 1

Version 2

Pseudomonas aeruginosa

PA 01

Version 2

Version 1

Rickettsia prowazekii

Madrid E

Wilmington

Version 1

Salmonella typhimurium/typhi

LT2

CT18

Ty2

Version 5

Version 1

Version 2

Version 4

Staphylococcus aureus

COL

MU50

MW2

N315

MRSA252

MSSA476

pLW043

Version 6

Version 1

Version 2

Version 4

Version 5

Streptococcus agalactiae

NEM316

2603V/R

A909

Version 2

Version 1

Streptococcus mutans

UA159

Version 1

Version 2

Streptococcus pneumoniae

TIGR4

R6

G54

Bacteriophage MM1

Version 7

Version 1

Version 2

Version 4

Version 5

Version 6

Streptococcus pyogenes

SSI-1

MGAS315

MGAS2096

MGAS5005

MGAS6180

MGAS8232

MGAS9429

MGAS10270

MGAS10394

MGAS10750

SF370

plasmid pDN571 (71-724)

Version 1

Streptococcus sanguinis

SK36

Version 1

Test Microarray

Streptococcus pneumoniae TIGR4

Staphylococcus aureus COL

Salmonella typhimurium LT2

Version 1

Treponema denticola

ATCC 35405

Version 1

Trypanosoma brucei

TREU927

Version 3

Version 1

Version 2

Trypanosoma cruzi

CL Brener TC3

Version 2

Version 1

Vibrio cholerae

el tor N16961

Version 1

Version 2

Vibrio parahaemolyticus

AQ3810

RIMD 2210633

plasmid pO3K6 (strain KXV237)

Version 1

Vibrio vulnificus

YJ016

CMCP6

Version 1

Yersinia pestis

CO-92

KIM

Version 3

Version 1

Version 2