Tag: Search

RNATOPS 1.2 – RNA Pseudoknot Search in Genomes

RNATOPS 1.2

:: DESCRIPTION

RNATOPS (RNA via Tree decOmPoSition) is a program that searches for RNA secondary structures based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Complier

:: DOWNLOAD

 RNATOPS

:: MORE INFORMATION

Citation

Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008)
Fast and accurate search for non-coding RNA pseudoknot structures in genomes,
Bioinforamtics, 24(20):2281-2287.

CoCo v2.0.1 – Search, Visualise and Store different data associated with Gene Expression

CoCo v2.0.1

:: DESCRIPTION

CoCo (ChIP-on-Chip online) is a computational tool that allows the user to search, visualise and store different data associated with gene expression.

::DEVELOPER

The Furlong Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java
  • Ant
  • Tomcat
  • MySQL
  • R
  • BioConductor

:: DOWNLOAD

 CoCo

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Mar 15;23(6):771-3. Epub 2007 Jan 17.
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.
Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE.

PNNS – Protein Network Neighbor Search

PNNS

:: DESCRIPTION

PNNS allows the user to quickly find nodes closest to a queried vertex in any protein network available from BioGRID or specified by the user.

::DEVELOPER

Computational Biology Laboratory – Boston University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  PNNS

:: MORE INFORMATION

Citation

BMC Syst Biol. 2009 Nov 29;3:112. doi: 10.1186/1752-0509-3-112.
Spectral affinity in protein networks.
Voevodski K, Teng SH, Xia Y.

PMSearch – Poly Matrix Search

PMSearch

:: DESCRIPTION

PMSearch (Poly Matrix Search) is a tool that utilizes Position Weight Matrices to search for putative Transcription Factor Binding Sites. PMSearch takes Position Frequency Matrices (PFMs) and DNA sequences to initiate a prediction task. The user may upload motifs/matrices (Position Frequency Matrices, PFM or Position Weight Matrices, PWM))or retrieve PFMs from our local dataset as input. We currently have 507 PFMs downloaded from Transfac Public Database 7.0 and JASPAR. Besides PFMs, the user may add multiple sequences in FASTA or Genbank format. PMSearch outputs a plot, a table of location, score and motif of each high scoring site and clusters of these sites.

::DEVELOPER

Bioinformatics Group in Nanjing University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2006 Jun 15;1(5):156-7.
A web server for transcription factor binding site prediction.
Su G, Mao B, Wang J.

ChAT – Unsupervised algorithm to Search Combinatorial Chromatin Signatures.

ChAT

:: DESCRIPTION

ChAT (Chromatin-profile Alignment followed by Tree-clustering algorithm) employs dynamic programming of combinatorial histone modification profiles to identify locally similar chromatin sub-regions and provides complementary utility with respect to existing methods.

::DEVELOPER

Jordan Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • R Program

:: DOWNLOAD

  ChAT

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov;40(21):10642-56. doi: 10.1093/nar/gks848. Epub 2012 Sep 18.
Chromatin signature discovery via histone modification profile alignments.
Wang J, Lunyak VV, Jordan IK.

SNPHunter 1.75 – dbSNP Search & Management

SNPHunter 1.75

:: DESCRIPTION

SNPHunter is a tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering.

::DEVELOPER

Program for Population Genetics

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SNPHunter

:: MORE INFORMATION

Citation

Lin Wang, Simin Liu, Tianhua Niu, Xin Xu (2005).
SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management.
BMC bioinformatics. 6: 60.

SMaRTFinder DR4 – Search Biosequences for Structured Motifs

SMaRTFinder DR4

:: DESCRIPTION

 SMaRTFinder is a command line tool to search biosequences for structured motifs (or structured models), that is lists of patterns separated by distance intervals.

::DEVELOPER

Nicola Vitacolonna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SMaRTFinder

:: MORE INFORMATION

ProSMoS – Protein Structure Motif Search

ProSMoS

:: DESCRIPTION

ProSMoS searches for 3D patterns in protein structures, e.g. find all proteins with a fold defined by a user.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ProSMoS

:: MORE INFORMATION

Citation:

S-Y.Shi, B.Chitturi, and N.V.Grishin (2009)
“ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.”
Nucl. Acids Res. (2009) doi: 10.1093/nar/gkp316 First published online: May 6, 2009

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