Re-searcher 1.4 – System for Recurrent Searches of Homologs in Protein Sequence databases

Re-searcher 1.4

:: DESCRIPTION

Re-searcher is a user-friendly configurable system for recurrent searches and reporting of new homologs in specified protein sequence databases. Searches can be performed at desired intervals either within NCBI or local databases using BLAST or PSI-BLAST. In addition to searches against an individual database, the system can perform “PDB-BLAST”-like combined searches, when PSI-BLAST profile generated during search against the first database is used to search the second database. The system supports multiple users each keeping track of multiple queries and query-specific results.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

Researcher

::REQUIREMENTS

  • Windows/Linux
  • Web Server
  • Java

:: DOWNLOAD

  Re-searcher

:: MORE INFORMATION

Citation

Repšys V., Margelevičius M. and Venclovas Č. (2008)
Re-searcher: a system for recurrent detection of homologous protein sequences.
BMC Bioinformatics 2008, 9:296

Ibis 1.1.7 – Improved Base Identification system for the Illumina Genome Analyzer

Ibis 1.1.7

:: DESCRIPTION

Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology.

::DEVELOPER

Department of Genetics / Bioinformatics Group, Max Planck Institute for Evolutionary Anthropology, Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SOAP

:: DOWNLOAD

   Ibis

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.
Improved base calling for the Illumina Genome Analyzer using machine learning strategies.
Kircher M, Stenzel U, Kelso J.

Gorgon 2.2.0 – Molecular Modeling system

Gorgon 2.2.0

:: DESCRIPTION

Gorgon is an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

::DEVELOPER

Media and Machines Lab at Washington University in St. Louis and National Center for Macromolecular Imaging at Baylor College of Medicine 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows  / Linux / MacOsX

:: DOWNLOAD

 Gorgon

:: MORE INFORMATION

Citation

J Struct Biol. 2011 May;174(2):360-73. Epub 2011 Feb 4.
Modeling protein structure at near atomic resolutions with Gorgon.
Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T.

BiVeS 1.7.3 – Biochemical Model Version Control System

BiVeS 1.7.3

:: DESCRIPTION

BiVeS (Biochemical Model Version Control System) is a library to detect differences between two versions of a computational model.

:: DEVELOPER

BiVeS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 BiVeS

:: MORE INFORMATION

Citation

Improving the reuse of computational models through version control
Dagmar Waltemath; Ron Henkel; Robert H?lke; Martin Scharm; Olaf Wolkenhauer
Bioinformatics 2013; doi: 10.1093/bioinformatics/btt018

AceDB 4.9.62 – Genome Database System

AceDB 4.9.62

:: DESCRIPTION

AceDB (A C. elegans DataBase) is a genome database designed specifically for handling bioinformatic data flexibly. It includes tools designed to manipulate genomic data, but is increasingly also used for non-biological data. Written originally for the C. elegans sequencing project, the software is used to manage genetical and physical map data and DNA sequences from a variety of plants, animals and prokaryotes.

::DEVELOPER

by Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger Institute).

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • GTK

:: DOWNLOAD

AceDB for Mac/Linux , for win

:: MORE INFORMATION

Citation:

Stein, L.D. Thierry-Mieg, J.
AceDB: a genome database management system
Computing in Science & Engineering ,1 Issue: 3 ,p44 – 52

PaVESy 20060803 – Pathway Visualization Editing System

PaVESy 20060803

:: DESCRIPTION

 PaVESy allows user-driven, interactive creation and visualization of pathway maps.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 PaVESy

:: MORE INFORMATION

Citation

A. Luedemann, D. Weicht, J. Selbig, J. Kopka (2004)
PaVESy: Pathway Visualization and Editing System.
Bioinformatics 2004 20(16): 2841-2844

Tclass – Tumor Classification System based on Gene Expression Profile

Tclass

:: DESCRIPTION

The Tclass system was developed for gene expression profile-based tumor classification. The results indicate that the number of genes for early detection of breast cancer is less than 10.

::DEVELOPER

Center of Computational Biology, Beijing Institute of Basic Medical Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

  Tclass

:: MORE INFORMATION

Citation

Li WJ, Xiong MM:
Tclass: tumor classification system based on gene expression profile.
Bioinformatics 2002, 18:325-326

GPSy – Gene Prioritization System for Conserved Biological Processes

GPSy

:: DESCRIPTION

GPSy (gene prioritization system) is a high-throughput profiling experiments based on for example microarrays or proteomics yield genes potentially important for a given biological process.

::DEVELOPER

GenOuest

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W458-65. doi: 10.1093/nar/gks380. Epub 2012 May 8.
GPSy: a cross-species gene prioritization system for conserved biological processes–application in male gamete development.
Britto R, Sallou O, Collin O, Michaux G, Primig M, Chalmel F.

SSPred – Identification & Classification of Proteins involved in Bacterial Secretion Systems

SSPred

:: DESCRIPTION

SSPred is a prediction server for the identification & classification of proteins involved in bacterial secretion systems

::DEVELOPER

Sachin Pundhir

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pundhir, S., and Kumar, A. (2011)
SSPred: a prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems.
Bioinformation 6(10): 380-382

EGene 1.0 – Automated Pipeline Generation System for Sequence Analysis

EGene 1.0

:: DESCRIPTION

EGene is a generic, flexible and modular pipeline generation system that makes pipeline construction a modular job. EGene allows for third-party programs to be used and integrated according to the needs of distinct projects and without any previous programming or formal language experience being required.

Coed is a visual tool to facilitate pipeline construction and documentation.

::DEVELOPER

EGene Team

:: SCREENSHOTS

EGene

:: REQUIREMENTS

  • Linux
  • Java
  • Perl
  • PostgreSQL

:: DOWNLOAD

  EGene , Coed

:: MORE INFORMATION

Citation:

Durham, A.M.; Kashiwabara, A.Y.; Matsunaga, F.T.; Ahagon, P.H.; Rainone, F.; Varuzza, L. & Gruber A. (2005).
EGene: a configurable pipeline generation system for automated sequence analysis. 
Bioinformatics 21(12): 2812-2813.