CoBaltDB 1.0 – Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database

CoBaltDB 1.0

:: DESCRIPTION

CoBaltDB (Complete Bacterial and Archaeal Orfeomes Subcellular Localization Database) which aims at presenting the cellular localisation of all prokaryotic proteins of all sequenced genomes, as predicted by numerous bioinformatic localisation tools.

::DEVELOPER

B@SIC (Bioinformatics Applied to Stresses and Cellular Interactions)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java

:: DOWNLOAD

  CoBaltDB

:: MORE INFORMATION

Citation

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F.
BMC Microbiol. 2010 Mar 23;10:88.

eBLOCKS – Database of Conserved Protein Regions

eBLOCKS

:: DESCRIPTION

eBLOCKS is a database of 80,000 conserved protein regions from 20,000 aligned protein families assembled using PSI-BLAST. eBLOCKs lets you compare new proteins to this database of conserved sequences using either eMOTIFs or eMATRICES made from eBLOCKs.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

  eBLOCKS

:: MORE INFORMATION

Citation:

Qiaojuan Jane Su, Lin Lu, Serge Saxonov and Douglas L. Brutlag
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
Nucl. Acids Res. (2005) 33 (suppl 1): D178-D182.

eSIGNAL 1.0 – Database of Medline MeSh Terms & Protein Motifs that Detect Signal Transduction Proteins

eSIGNAL 1.0.0

:: DESCRIPTION

eSignal is a database of eMOTIFs and eMATRICES generated exclusively from signal transduction proteins. ESIGNAL can be used to discover signal transduction functions in new proteins.

::DEVELOPER

 The Brutlag Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier
  • Perl

:: DOWNLOAD

   eSIGNAL

:: MORE INFORMATION

 

SeqHound 3.02 – Bioinformatics Database Warehouse Resource

SeqHound 3.02

:: DESCRIPTION

SeqHound is a freely available bioinformatics database warehouse resource that collects bioinformatics data from a number of sources including the National Center for Biotechnology Information and the Gene Ontology Consortium. It is designed for programmers who need unrestricted access to up-to-date data.

::DEVELOPER

Department of Biochemistry, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • Java

:: DOWNLOAD

 SeqHound

:: MORE INFORMATION

Citation

Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.
SeqHound: biological sequence and structure database as a platform for bioinformatics research.
BMC Bioinformatics. 2002 Oct 25;3:32. Epub 2002 Oct 25.

ARCADE 0.1 beta – Query and Visualize Data from Multiple Databases

ARCADE 0.1 beta

:: DESCRIPTION

ARCADE (A Real Time Comparative Analysis Display Environment) performs comparative queries over two or more distributed and potentially heterogeneous databases.The existence of large amounts of genomic information from many species on different databases means that sophisticated tools are required to retrieve the information important to a user and to display it a coherent manner. Furthermore, since information about one species can be used to aid research on closely related species there is great need for tools to be able to perform complex comparative queries. For example, the conserved gene order found in some cereals may be exploited to locate homologous genes in related species. ARCADE is a software tool for carrying out such comparative queries across many different sources and to display the results of these queries in a suitable coherent format.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 ARCADE

:: MORE INFORMATION

Citation:

Couchman M, Davenport G and Dicks J (2002)
A real-time comparative analysis display environment (ARCADE).
Genome Informatics, Hinxton

PersonalGenBank 200610 – Local Sequence Database

PersonalGenBank 200610

:: DESCRIPTION

PersonalGenBank is a database software maintaining sequences and sequence information in GenBank-format. Generally, the user downloads a large chunk of sequences from GenBank to the local computer and then imports these sequences into PersonalGenBank.

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PersonalGenBank

:: MORE INFORMATION

Request a free trial license to use the full spectrum of features for one month and free of charge!

EcoLens 20051212 – Browse through a Large Database of Information about Food Webs

EcoLens 20051212

:: DESCRIPTION

EcoLens allows biologists to browse through a large database of information about food webs, find webs of interest, and then visualize links using TreePlus (see below).  It is essentially a front end to relational data tables that offers coupled interaction, searching, and simple bar chart visualization to replace complex queries.

::DEVELOPER

Biodiversity Informatics Visualization TeamHuman-Computer Interaction Lab , University of Maryland

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows with .NET

:: DOWNLOAD

EcoLens

:: MORE INFORMATION

MPtopoQuerier – Search Database of Membrane Proteins

MPtopoQuerier

:: DESCRIPTION

MPtopoQuerier is a java applet developed for searching MPtopo, a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool.

::DEVELOPER

Stephen White laboratory at UC Irvine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

MPtopoQuerier

:: MORE INFORMATION

Citation

Jayasinghe, S., Hristova, K., and White, S. H. (2001).
MPtopo: A database of membrane protein topology.
Protein Sci 10:455-458.

ProtBuD – Protein Biological Unit Database

ProtBuD

:: DESCRIPTION

ProtBuD (Protein Biological Unit Database) is a new database of asymmetric units (ASU) and biological units (BU) from PDB and PQS, and uses SCOP and PSIBLAST to provide ASU and BU for all entries with proteins in particular superfamilies or families. It allows the user to search the SCOP database for a particular entry, retrieve the asymmetric and biological units for almost all related proteins in the same SCOP category, compare side-by-side the biological units designated by PDB and PQS, analyze the protein interfaces, and download quickly and conveniently the structure files of interest.

ProtBuD Online Version

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ProtBuD

:: MORE INFORMATION

N/A

BOXIT 2007 – Database for Molecular Biology Laboratories

BOXIT 2007

:: DESCRIPTION

BOXIT is an easy to use database that helps collect, store and organize information about all your antibodies, cells, oligos, plasmids and other biological samples.

::DEVELOPER

Bernd Wollscheid – BOXIT Developer – BOXIT LabSoftware

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

BOXIT

:: MORE INFORMATION

Price