Tag: Search Tool

GEOmetadb 1.52.0 – GEO Microarray Search Tool

GEOmetadb 1.52.0

:: DESCRIPTION

GEOmetadb is an attempt to make access to the metadata associated with the NCBI Gene Expression Omnibus (GEO) samples, platforms, and datasets much more feasible for common biologists and bioinformatians/statistians.

::DEVELOPER

Jack Zhu , Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOmetadb

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 1;24(23):2798-800. doi: 10.1093/bioinformatics/btn520.
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y.

STEPP – Search Tool for Exploration of Petri net Paths

STEPP

:: DESCRIPTION

STEPP is a tool programmed to performe paths searchs in (metabolic) petri nets.

::DEVELOPER

Molecular Bioinformatics MolBI

:: SCREENSHOTS

STEPP1

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 STEPP

:: MORE INFORMATION

Citation

In Silico Biol. 2005;5(2):129-37.
STEPP–Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks.
Koch I1, Schueler M, Heiner M.

BEST 1.0 – Bayesian Expression Search Tool

BEST 1.0

:: DESCRIPTION

BEST (Bayesian Expression Search Tool) implements a model-based Bayesian querying tool. This program is designed to query large and heterogeneous microarray gene expression database. It is able to identify a small set of genes that share correlated gene expression profiles with the query gene under a subset of samples/experimental conditions. In addition, it allows linearly transformed expression patterns to be recognized and is robust against sporadic outliers in the data.

::DEVELOPER

Ming Hu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BEST

:: MORE INFORMATION

Citation

Ming Hu, Zhaohui S. Qin
Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection
PLoS One. 2009;4(2):e4495. Epub 2009 Feb 13.

Bang – Repeat-supressing Search Tool

Bang

:: DESCRIPTION

Bang is a fast repeat-supressing search tool, written primarily for anchoring reads to genomes but also adaptable to other genome scale comparison problems.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX

:: DOWNLOAD

Bang

:: MORE INFORMATION

CLAST 0.1.5 – CUDA implemented large-scale Alignment search tool

CLAST 0.1.5

:: DESCRIPTION

CLAST (CUDA implemented large-scale alignment search tool) is a tool that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units.

::DEVELOPER

CLAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CLAST

:: MORE INFORMATION

Citation

CLAST: CUDA implemented large-scale alignment search tool.
Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K.
BMC Bioinformatics. 2014 Dec 11;15:406. doi: 10.1186/s12859-014-0406-y.

GHOST-MP 1.3.4 – Parallel Sequence Similarity Search Tool

GHOST-MP 1.3.4

:: DESCRIPTION

GHOST-MP is a parallel sequence similarity search tool. It searches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX.

::DEVELOPER

Akiyama Laboratory , Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

GHOST-MP

:: MORE INFORMATION

Citation

Int J Mol Sci. 2017 Oct 11;18(10). pii: E2124. doi: 10.3390/ijms18102124.
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data.
Kakuta M, Suzuki S, Izawa K, Ishida T, Akiyama Y

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.

STITCH 5.0 – Search Tool for Interactions of Chemicals and proteins

STITCH 5.0

:: DESCRIPTION

STITCH (search tool for interactions of chemicals)  is a resource to explore known and predicted interactions of chemicals and proteins.Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

 STITCH

:: MORE INFORMATION

Citation

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.
Nucleic Acids Res. 2015 Nov 20. pii: gkv1277.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M1, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P
Nucleic Acids Res. 2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.

Peppy – Proteogenomic, Proteomic search tool

Peppy

:: DESCRIPTION

Peppy: a fully integrated, proteogenomic mapping software tool. Peppy generates a peptide database from genome files, tracks peptide loci, matches peptides to MS/MS spectra, assigns scores to those matches, and tracks score distributions to find E-Values. To determine false discovery rate thresholds, Peppy automatically generates a decoy database from the original genome files and repeats the entire search process.

::DEVELOPER

The Giddings Lab at Boise State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Peppy

:: MORE INFORMATION

Citation

Peppy: proteogenomic search software.
Risk BA, Spitzer WJ, Giddings MC.
J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w.

FingerPRINTScan – PRINTS Fingerprint Search Tool

FingerPRINTScan

:: DESCRIPTION

The FingerPRINTScan package uses an approach, based on Karlin and Altschul statistics, to generate a probability-value for each scoring match to a motif.

::DEVELOPER

Attwood Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 FingerPRINTScan 

:: MORE INFORMATION

Citation

Bioinformatics. 1999 Oct;15(10):799-806.
FingerPRINTScan: intelligent searching of the PRINTS motif database.
Scordis P, Flower DR, Attwood TK.