Datasets2Tools – Repository and Search Engine for Bioinformatics Datasets, Tools and Canned Analyses

Datasets2Tools

:: DESCRIPTION

Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

datasets2tools

:: MORE INFORMATION

Citation

Sci Data. 2018 Feb 27;5:180023. doi: 10.1038/sdata.2018.23.
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.
Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma’ayan A.

GeNemo – Web-based Search Engine for Functional Genomic Data

GeNemo

:: DESCRIPTION

GeNemo is a search engine for functional genomic data. GeNemo searches user-input data against online functional genomic datasets, including the entire collection of ENCODE and mouse ENCODE datasets

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

GeNemo: a search engine for web-based functional genomic data.
Zhang Y, Cao X, Zhong S.
Nucleic Acids Res. 2016 Jul 8;44(W1):W122-7. doi: 10.1093/nar/gkw299.

PepQuery 1.3.0 – Peptide-centric Search Engine for novel Peptide searching

PepQuery 1.3.0

:: DESCRIPTION

PepQuery is a peptide-centric search engine that allows quick and easy proteomic validation of genomic alterations without customized database construction.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PepQuery

:: MORE INFORMATION

Citation

Genome Res. 2019 Mar;29(3):485-493. doi: 10.1101/gr.235028.118. Epub 2019 Jan 4.
PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations.
Wen , Wang X, Zhang B.

GEMINI – The Genomic Search Engine

GEMINI

:: DESCRIPTION

GEMINI is an open-source bioinformatics tool and website written in python to facilitate near-neighbor searching of genomic data.

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GEMINI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Feb 24;17:102. doi: 10.1186/s12859-016-0934-8.
GEMINI: a computationally-efficient search engine for large gene expression datasets.
DeFreitas T, Saddiki H, Flaherty P

MSblender – Integrating Peptide Identifications from multiple database search engines

MSblender

:: DESCRIPTION

MSblender is a software for integrating peptide identifications from multiple database search engines. MSblender rescores unique peptide-spectrum matches by multivariate mixture modeling of score distributions from multiple search engines.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 MSblender 

:: MORE INFORMATION

Citation:

T. Kwon, H. Choi, C. Vogel, A.I. Nesvizhskii, and E.M. Marcotte,
MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines.
J. Proteome Res., 2011, 10 (7), pp 2949–2958

Giggle v0.6.3 – Search Engine for large-scale integrated Genome Analysis

Giggle v0.6.3

:: DESCRIPTION

Giggle is a genomics search engine for genomic features and intervals. That is, scalable, multi-file index for fast queries of genomic intervals.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Giggle

:: MORE INFORMATION

Citation:

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.
GIGGLE: a search engine for large-scale integrated genome analysis.
Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR

RNA FRABASE 2.0 – RNA FRAgment Search Engine & Database

RNA FRABASE 2.0

:: DESCRIPTION

RNA FRABASE: an engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 May 6;11:231. doi: 10.1186/1471-2105-11-231.
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.
Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW.

PeptideShaker 1.1.3 – Interpretation of Proteomics Identifications from multiple search engines

PeptideShaker 1.1.3

:: DESCRIPTION

PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 PeptideShaker

:: MORE INFORMATION

Citation

Acta Neurol Scand Suppl. 2012;(195):90-6. doi: 10.1111/ane.12029.
Cerebrospinal fluid proteome comparison between multiple sclerosis patients and controls.
Kroksveen AC, Guldbrandsen A, Vedeler C, Myhr KM, Opsahl JA, Berven FS.

MRS 6.0.5 – Search Engine for Biological and Medical Databanks

MRS 6.0.5

:: DESCRIPTION

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

::DEVELOPER

Centre for Molecular and Biomolecular Informatics(CMBI), Radboud University Nijmegen Medical Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Web Server
  • Perl

:: DOWNLOAD

 MRS

:: MORE INFORMATION

Citation:

Hekkelman M.L., Vriend G.
MRS: A fast and compact retrieval system for biological data.
Nucleic Acids Research 2005 33(Web Server issue):W766-W769;