IGD – A high-performance Search Engine for large-scale Genomic Interval Datasets

IGD

:: DESCRIPTION

IGD (integrated genome database) is a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

IGD

:: MORE INFORMATION

Citation

Feng J, Sheffield NC.
IGD: high-performance search for large-scale genomic interval datasets.
Bioinformatics. 2020 Dec 26:btaa1062. doi: 10.1093/bioinformatics/btaa1062. Epub ahead of print. PMID: 33367484.

DigSee v2.01 – Disease Gene Search Engine with Evidence Sentence

DigSee v2.01

:: DESCRIPTION

DigSee is a text mining search engine to provide evidence sentences describing that “genes” are involved in the development of “disease” through “biological events”. Biological events such as gene expression, regulation, phosphorylation, localization, and protein catabolism play important roles in the development of diseases. Understanding the association between diseases and genes can be enhanced with the identification of involved biological events in this association. With input of (disease, genes, events), users can obtain Medline abstracts with highlighted evidence sentences.

::DEVELOPER

Data Mining & Computational Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Kim J, So S, Lee HJ, Park JC, Kim JJ, Lee H.
DigSee: Disease gene search engine with evidence sentences (version cancer).
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W510-7. doi: 10.1093/nar/gkt531. Epub 2013 Jun 12. PMID: 23761452; PMCID: PMC3692119.

LAILAPS – Search Engine for Life Science data

LAILAPS

:: DESCRIPTION

LAILAPS combines a keyword driven search engine for an integrative access to life science databases, machine learning for a content driven relevance ranking, recommender systems for suggestion of related data records and query refinements with a user feedback tracking system for an self learning relevance training

::DEVELOPER

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 LAILAPS

:: MORE INFORMATION

Citation

M. Lange et al.
The LAILAPS Search Engine: Relevance Ranking in Life Science Databases
Journal of Integrative Bioinformatics. 7(2), 2010:

PepQuery 1.6.2 – Peptide-centric Search Engine for novel Peptide searching

PepQuery 1.6.2

:: 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.

piRNA 3.6 / biRNA 3.6 – RNA Interaction Search Engine

piRNA 3.6 / biRNA 3.6

:: DESCRIPTION

piRNA is a parallel C++ package to compute joint and individual partition functions for two RNA sequences. From the partition functions, piRNA computes equilibrium concentrations of single and double joint species, ensemble energy, and melting temperatures.

biRNA is a fast open source tool based on a heuristic algorithm to compute RNA-RNA binding sites.

:DEVELOPER

Algorithmic Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 piRNA

:: MORE INFORMATION

Citation

Hamidreza Chitsaz, Raheleh Salari, S. Cenk Sahinalp, Rolf Backofen
A Partition Function Algorithm for Interacting Nucleic Acid Strands
Bioinformatics (2009) 25 (12): i365-i373.

Genevestigator 8.3.2 – Gene Expression Search Engine

Genevestigator 8.3.2

:: DESCRIPTION

Genevestigator is a multi-organism microarray database and expression meta-analysis tool.Genevestigator is a high performance search engine for gene expression. Our focus is on the deep integration of high quality, well annotated data with high-performance computing. This allows users to run unique types of queries across thousands of datasets simultaneously.

::DEVELOPER

Genevestigator Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 Genevestigator

:: MORE INFORMATION

Citation

Hruz T, Laule O, Szabo G, Wessendrop F, Bleuler S, Oertle L, Widmayer P, Gruissem W and Zimmermann P (2008)
Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes.
Adv Bioinformatics vol. 2008, Article ID 420747, 5 pages. DOI: 10.1155/2008/420747

PeptideShaker v2.0.33 – Interpretation of Proteomics Identifications from multiple search engines

PeptideShaker v2.0.33

:: 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.

SIXPAC 1.0.2 – Search Engine for Genetic Interactions

SIXPAC 1.0.2

:: DESCRIPTION

SIXPAC is an efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.

::DEVELOPER

Snehit Prabhu at Itsik Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 SIXPAC

:: MORE INFORMATION

Citation:

Genome Res. 2012 Nov;22(11):2230-40. doi: 10.1101/gr.137885.112.
Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.
Prabhu S, Pe’er I.

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.

Exit mobile version