ARBitrator 1.0 – Retrieval of auto-curated nifH sequences from GenBank

ARBitrator 1.0

:: DESCRIPTION

ARBitrator is a pipeline for automated retrieval from GenBank of all sequences for a specified gene.

::DEVELOPER

Zehr Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 ARBitrator

:: MORE INFORMATION

Citation:

ARBitrator: A software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.
Heller P, Tripp HJ, Turk-Kubo K, Zehr JP.
Bioinformatics. 2014 Jul 2. pii: btu417

STRING 10 – Search Tool for the Retrieval of Interacting Genes/Proteins

STRING 10

:: DESCRIPTION

STRING (search tool for recurring instances of neighbouring genes) is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003

Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A1, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.

STRING 8–a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. Epub 2008 Oct 21.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2.

GDFuzz3D – Protein 2D Map to 3D Structure Retrieval Service

GDFuzz3D

:: DESCRIPTION

GDFuzz3D is a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.

::DEVELOPER

Bujnicki Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GDFuzz3D

:: MORE INFORMATION

Citation

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
Pietal MJ, Bujnicki JM, Kozlowski LP.
Bioinformatics. 2015 Jun 30. pii: btv390.

Qualiseq 20150216 – Quality Genomic Sequence Retrieval

Qualiseq 20150216

:: DESCRIPTION

QualiSeq is a Quality Genomic Sequence Retrieval Tool.

::DEVELOPER

Qualiseq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yu-Chang Cheng, Tz-Chao Lin, Kuo-His Lee, Yan-Hau Chen, Ming-Fang Tsai, Yi-Jung Lin, and Adam Yao (2006)
Qualiseq: Quality Genomic Sequence Retrieval,
Journal of Genetics and Molecular Biology Vol. 17, No. 4, 204-210, December 1, 2006

PDART – Protein Domain Architecture Retrieval Tool

PDART

:: DESCRIPTION

PDART is a web site to compare domain architectures or proteins.

:: DEVELOPER

Laboratory of Computational Molecular Biology, Beijing Normal University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Sep 1;22(17):2081-6. Epub 2006 Jul 12.
An initial strategy for comparing proteins at the domain architecture level.
Lin K1, Zhu L, Zhang DY.

SNPack 1.0 – Compression and fast Retrieval of SNP data

SNPack 1.0

:: DESCRIPTION

SNPack is a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies.

::DEVELOPER

Francesco Sambo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SNPack

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu495.
Compression and fast retrieval of SNP data.
Sambo F, Di Camillo B, Toffolo G, Cobelli C.

KiPar – Systematic Information retrieval regarding parameters for Kinetic Modelling of Metabolic Pathways

KiPar

:: DESCRIPTION

KiPar is a standalone Java application for the retrieval of textual documents likely to contain information relevant for kinetic modelling of a given metabolic pathway.

::DEVELOPER

The Manchester Centre for Integrative Systems Biology(MCISB)

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java
  • PostgreSQL

:: DOWNLOAD

 KiPar

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 1;25(11):1404-11. doi: 10.1093/bioinformatics/btp175. Epub 2009 Mar 31.
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.
Spasic I1, Simeonidis E, Messiha HL, Paton NW, Kell DB.

MaRe – Searching and large scale Retrieval of public Microarray data

MaRe

:: DESCRIPTION

MaRe (Microarray Retriever) enables batch retrieval of microarray data matching your search criteria from the seas of data in GEO and ArrayExpress microarray repositories. You can search on accession numbers (GSE, GDS, AE_ACCN, PMID), authors, species, dates, platforms or on keywords of unspecified type.

::DEVELOPER

Microarray Analysis Group, Center for Human and Clinical Genetics – LUMC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W327-31. doi: 10.1093/nar/gkn213. Epub 2008 May 7.
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data.
Ivliev AE1, ‘t Hoen PA, Villerius MP, den Dunnen JT, Brandt BW.

MARS 1.2.0 – Microarray Analysis and Retrieval System

MARS 1.2.0

:: DESCRIPTION

 MARS (Microarray Analysis and Retrieval System) provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a lab notebook, a laboratory information management system (LIMS), a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

  MARS

:: MORE INFORMATION

Citation

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z.
MARS: microarray analysis, retrieval, and storage system.
BMC Bioinformatics. 6: 101-101 (2005)

RRE 20040401 – Retrieval of Non-coding Regulative Elements from Annotated Genomic databases

RRE 20040401

:: DESCRIPTION

RRE (Retrieval of non-coding Regulative Elements) is a tool to extract non-coding regions associated to annotated genes.

RRE Online Version

::DEVELOPER

the Bioinformatics and Genomics Unit at Dept. of Clinical and Biological Sciencesat Torino University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  •  Java

:: DOWNLOAD

 RRE

:: MORE INFORMATION

Citation:

Bioinformatics. 2004 Nov 1;20(16):2848-50. Epub 2004 Apr 29.
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets.
Lazzarato F, Franceschinis G, Botta M, Cordero F, Calogero RA.