Tag: Retrieval

Refget v0.1.0 – Refget Sequence Identification and Retrieval

Refget v0.1.0

:: DESCRIPTION

Refge is a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Refget

:: MORE INFORMATION

Citation

Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM.
Refget: standardised access to reference sequences.
Bioinformatics. 2021 Jul 14:btab524. doi: 10.1093/bioinformatics/btab524. Epub ahead of print. PMID: 34260694.

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

MaRe team

:: 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.

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

SYSTEMS BIOLOGY AND BIOINFORMATICS GROUP

:: 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.

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.

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 11.0 – Search Tool for the Retrieval of Interacting Genes/Proteins

STRING 11.0

:: 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.

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.

MitoBank 2.1 – Automatic Retrieval and Parsing of Mitochondrial Genomes

MitoBank 2.1

:: DESCRIPTION

MitoBank is a simple perl script to obtain from GeneBank mitochondrial genomes, parse them, and store the different genes in separate files. It can be used to retrieve both coding genes and RNA genes. Coding genes might be obtained in their amino acid or nucleotide sequence.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MitoBank

:: MORE INFORMATION

Citation:

Abascal F, Posada D, Zardoya R. (2007)
MtArt: A new model of amino acid replacement for Arthropoda.
Molecular Biology and Evolution 24: 1-5.

ORFer 1.3.2.2 – Retrieval of Protein Sequences and Open Reading Frames from GenBank

ORFer 1.3.2.2

:: DESCRIPTION

ORFer (Open Reading Frame Retrieval) reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.The open reading frame corresponding to the protein sequences is extracted from the XML and displayed. ORFer has a database interface that allows for storing the retrieved sequences in a local SQL database.

::DEVELOPER

Konrad Büssow and Steve Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

ORFer

:: MORE INFORMATION

Citation

Konrad Büssow , Steve Hoffmann and Volker Sievert
ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
BMC Bioinformatics 2002, 3:40doi:10.1186/1471-2105-3-40