Tag: Computational Tool

CanPredict – Computational tool for Predicting Cancer-associated Mutations

CanPredict

:: DESCRIPTION

CanPredict uses a combination of computational methods to identify those changes most likely to be cancer-associated. Paste your sequence and change(s) below to generate a prediction.

::DEVELOPER

Josh Kaminker (kaminker@gene.com) or Yan Zhang (yz5@gene.com) in Dr. Zemin Zhang’s group in the Bioinformatics department at Genentech.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

CanPredict: a computational tool for predicting cancer-associated missense mutations.
Kaminker JS, Zhang Y, Watanabe C, Zhang Z.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W595-8.

MOITF-EM – Automated Computational Tool for Identifying Conserved Domains in CryoEM Structures

MOITF-EM

:: DESCRIPTION

MOTIF-EM is an automated computational tool for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.)

::DEVELOPER

Mitul Saha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MOITF-EM 

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i301-9. doi: 10.1093/bioinformatics/btq195.
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.
Saha M, Levitt M, Chiu W.

QSB – Computational Tool for Genetical Genomics

QSB

:: DESCRIPTION

QSB (QTL mapping, Sequence polymorphism analysis (or SNP analysis) and Bayesian network) is a computational tool developed for genetical genomics, an emerging field that combines quantitative genetics and genomics. QSB takes marker genotype data and expression microarray data of a segregating population as input and identify the significant QTLs that module gene expression. DNA sequence polymorphism analysis and Bayesian Network (BN) is then used to further evaluate the candidate modulator genes in the QTL intervals. The modulatory relations that best explain the microarray data are used to construct gene modulatory networks. It has four modules: (1) transcriptome QTL (or eQTL) mapping, (2) DNA sequence polymorphism analysis, (3) inferring gene modulatory network using Bayesian network (BN) and (4) gene network visualization.

::DEVELOPER

Cui Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Java

:: DOWNLOAD

 QSB

:: MORE INFORMATION