Tag: Database

OncomiRDB – Database for the Experimentally Verified Oncogenic and Tumor-suppressive microRNAs

OncomiRDB

:: DESCRIPTION

OncomiRDB is a web-based portal, which provides both graphical and text-based interfaces, was developed for easily browsing and searching all the annotations. It should be a useful resource for both the computational analysis and experimental study on miRNA regulatory networks and functions in cancer.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 N/A

:: MORE INFORMATION

Citation

OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs.
Bioinformatics 2014, 30(15):2237-2238.
Dongfang Wang, Jin Gu#, Ting Wang, Zijian Ding.

InforBIO 5.28 – E-Workbench for Databasing, Classification & Identification of Microbes

InforBIO 5.28

:: DESCRIPTION

InforBIO is an e-Workbench for databasing, classification and identification of microbes. InforBIO can identify the phenotypic characteristics that discriminate and are associated with the clusters of a phylogenetic tree.

::DEVELOPER

WFCC-MIRCEN World Data Centre for Microorganisms

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 InforBIO

:: MORE INFORMATION

Citation

Hideaki Sugawara, Naoto Tanaka, and Satoru Miyazaki (2003)
An e-Workbench for the study of microbial diversity,
The system design and basic functions. Microbial. Cult. Coll., 19, 59-67 (InforBIO.pdf)

Database Manager 2.1 – FASTA Database Manager

Database Manager 2.1

:: DESCRIPTION

Database Manager stores all your sequence databases in a single folder (repository). It offers :

  • conservation of metadata : database origin, species, number of protein, download site, …
  • translation of DNA into protein
  • creation of decoy protein databases (protein reverse, random, peptide reverse
  • combination of different existing databases

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

Fastamanager

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 Database Manager

:: MORE INFORMATION

seeQTL – A Searchable Human eQTL Browser and database

seeQTL

:: DESCRIPTION

seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots.

::DEVELOPER

Department of Biostatistics, Computer Sciences and Genetics, University of North Carolina at Chapel Hill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web  Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

K. Xia, A.A. Shabalin, S. Huang, V. Madar, Y.H. Zhou, W. Wang, F. Zou, W. Sun, P.F. Sullivan, and F.A. Wright
seeQTL: A searchable database for human eQTLs
Bioinformatics (2012) 28(3): 451-452

Virusbanker 1.0 – MySQL database of Virus Sequences and Alignments

Virusbanker 1.0

:: DESCRIPTION

Virusbanker is a MySQL database of virus sequences and alignments that is accessed via a Java program.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

Virusbanker

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • MySQL

:: DOWNLOAD

 Virusbanker

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Feb 5;9:83. doi: 10.1186/1471-2105-9-83.
The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.
Fourment M, Gibbs MJ.

ACIB PGDB Toolbox 1.0 – Create, Maintain and Query Pathway/Genome Databases

ACIB PGDB Toolbox 1.0

:: DESCRIPTION

ACIB PGDB Toolbox is a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface (GUI) and menu of Pathway Tools, this plug-in provides functions to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyze their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various -omics viewers of Pathway Tools

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  ACIB PGDB Toolbox

:: MORE INFORMATION

Citation

Krempl PM, Mairhofer J, Striedner G, Thallinger GG.
A Sequence Comparison and Gene Expression Data Integration Add-on for the Pathway Tools Software.
Bioinformatics. 2012 Sep 1;28(17):2283-4.

BioWarehouse 4.6 – Database Integration for Bioinformatics

BioWarehouse 4.6

:: DESCRIPTION

BioWarehouse is a database interoperation environment that supports data mining and integration of multiple databases including the UniProt, BioCyc, NCBI Taxonomy, Genbank, CMR, ENZYME, Gene Ontology, and KEGG databases.

::DEVELOPER

BioWarehouse Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • MySQL

:: DOWNLOAD

 BioWarehouse

:: MORE INFORMATION

Citation

Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum3 and Peter D Karp
BioWarehouse: a bioinformatics database warehouse toolkit
BMC Bioinformatics 2006, 7:170

Biota 3.00 – Biodiversity Database Manager

Biota 3.00

:: DESCRIPTION

Biota manages specimen-based, spatially and taxonomically referenced data for ecologists, conservation biologists, evolutionary biologists, systematists, museums and herbaria.

::DEVELOPER

Robert K. Colwell

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 Biota

:: MORE INFORMATION

Citation

Colwell, R. K. 2004.
Biota 2: The biodiversity database manager.
Sinauer Associates, Sunderland, MA.

OperonDB 2.1 – Database of Predicted operons in Microbial Genomes

OperonDB 2.1

:: DESCRIPTION

OperonDB is a database containing the results of a computational algorithm for locating operon structures in microbial genomes. OperonDB has grown from 34 genomes in its initial release to more than 500 genomes today. In addition to increasing the size of the database, we have re-designed our operon finding algorithm and improved its accuracy.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 OperonDB

:: MORE INFORMATION

Citation:

M. Pertea et al.,
OperonDB: a comprehensive database of predicted operons in microbial genomes
Nucl. Acids Res 37 (2009), D479-D482.

RNAdbtool – Update and Cleanup of Structural RNA Databases

RNAdbtool

:: DESCRIPTION

RNAdbtool is a collection of tools which can be used to perform semi-automated update of RNA structural databases.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RNAdbtool

:: MORE INFORMATION

Citation:

Bioinformatics. 2001 Jul;17(7):642-5.
Semi-automated update and cleanup of structural RNA alignment databases.
Gorodkin J, Zwieb C, Knudsen B.