TAMO 20120321 – Analyze Transcriptional Regulation using DNA-sequence Motifs

TAMO 20120321

:: DESCRIPTION

TAMO  (Tools for Analysis of MOtifs) is developed around a unified motif representation of a position-specific scoring matrix (PSSM). Motif objects may be assembled from IUPAC-ambiguity codes, multiple sequence alignments, averages of other motifs, and matrices of frequencies or log-likelihood values. Motifs can printed, concatenated, indexed and sliced like text strings, or rendered as sequence logos. They can also be randomized, reverse-complemented, and recomputed using different assumptions about background base frequencies. Motifs can also store and report information about their origin, information content, and score. Finally, motifs can scan DNA sequences for instances of matching sites.

::DEVELOPER

The Fraenkel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 TAMO

:: MORE INFORMATION

Citation:

D. Benjamin Gordon, Lena Nekludova, Scott McCallum and Ernest Fraenke
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
Bioinformatics. 2005 Jul 15;21(14):3164-5.

Gemma 1.27.4 – Analyze Genomics data using Meta-analysis

Gemma 1.27.4

:: DESCRIPTION

Gemma is an open-source database and software system for the meta-analysis of gene expression data.

::DEVELOPER

Pavlidis lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Web Server

:: DOWNLOAD

 Gemma

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 15;25(12):1543-9. Epub 2009 Apr 17.
Application and evaluation of automated semantic annotation of gene expression experiments.
French L, Lane S, Law T, Xu L, Pavlidis P.

CGHweb 1.0 – Analyze Array_CGH data with Multiple Algorithms

CGHweb 1.0

:: DESCRIPTION

CGHweb is a tool that applies a number of popular algorithms to a single array CGH (comparative genomic hybridization) profile entered by the user. It generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. The clickable heatmap can be moved along the chromosome and zoomed in or out. It also displays the time that each algorithm took and provides numerical values of the segmented profiles for download

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CGHweb

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Apr 1;24(7):1014-5. Epub 2008 Feb 22.
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.
Lai W, Choudhary V, Park PJ.

AUTOSCAN 1.0.3 – Easy Genome-wide Scans with Analyze

AUTOSCAN 1.0.3

:: DESCRIPTION

AUTOSCAN automatically creates data files, uses MAKEPED (converts pre-linkage format files to linkage format), DOWNFREQ (estimates allele frequencies from pedigree data), and PEDCHECK (Mendelian checking) programs and finally starts statistical analyses via the ANALYZE package. ANALYZE performs parametric linkage analysis (MLINK), nonparametric affected sib-pair analysis (ASP), family-based association analysis (TDT, HRRR), and homogeneity testing (HOMOG). Input files for AUTOSCAN are the pedigree files for all chromosomes,the disease model file, the number of loci file, and the ANALYZE input file.The AUTOSCAN also allows easy handling of several phenotype traits and trait features by only changing the disease model file after each run.

::DEVELOPER

Tero Hiekkalinna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD AUTOSCAN

AUTOSCAN

:: MORE INFORMATION

N/A

eHAP 2.0 – Analyze Multilocus data as Haplotypes

eHAP 2.0

:: DESCRIPTION

The eHap software is designed to analyze multilocus data as haplotypes, and to determine whether there is an association between haplotypes and phenotypes. This version of eHap embodies a broad (and ever broadening) set of tools for haplotype-based inference for association (and linkage) studies using population- and family-based samples.

::DEVELOPER

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 eHap

:: MORE INFORMATION

 

GenEx 7.0 – Analyze Real-time qPCR Data

GenEx 7.0

:: DESCRIPTION

GenEx is a popular software for qPCR data processing and analysis. Built in a modular fashion GenEx provides a multitude of functionalities for the qPCR community, ranging from basic data editing and management to advanced cutting-edge data analysis.

::DEVELOPER

MultiD Analyses AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GenEx

:: MORE INFORMATION

Visual Gene Developer 1.9 – Gene Design software to Analyze, Design, and Optimize Genes

Visual Gene Developer 1.9

:: DESCRIPTION

Visual Gene Developer is a specialized gene design software that has many functions to analyze, design, and optimize genes. Originally, the software was developed to optimize DNA sequence (mainly for codon optimization) of our target genes and has been upgraded to be the general software package since 2008.

::DEVELOPER

Sang-Kyu Jung

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .Net (dot net) Framework 4.0

:: DOWNLOAD

 Visual Gene Developer

:: MORE INFORMATION

Citation

Jung, S.-K. and K. McDonald (2011).
Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization.”
BMC Bioinformatics 12(1): 340

imago 1.0.104 – Store, Organize, Search, and Analyze Scientific Images

imago 1.0.104

:: DESCRIPTION

Imago provides a browsable interface for collections of microscopy images, similar to iPhoto or Picasa. It also can be used to annotate images, create image mosaics, and identify and count cells.

::DEVELOPER

Mayachitra Inc.

:: SCREENSHOTS

imago

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 imago

:: MORE INFORMATION

LabKey Server 21.7 – Organize, Analyze, and Share Biomedical Research data

LabKey Server 21.7

:: DESCRIPTION

LabKey Server is open source software that helps scientists organize, analyze, and share biomedical research data.

::DEVELOPER

LabKey Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Apache Tomcat web server
  • SQL Server

:: DOWNLOAD

 LabKey Server

:: MORE INFORMATION

Citation

Elizabeth K Nelson et al.
LabKey Server: An open source platform for scientific data integration, analysis and collaboration
BMC Bioinformatics. 2011; 12: 71.

FragmentationAnalyzer 1.5.17 – Analyze MS/MS Fragmentation Data

FragmentationAnalyzer 1.5.17

:: DESCRIPTION

Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data.

::DEVELOPER

Harald Barsnes

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 FragmentationAnalyzer

:: MORE INFORMATION

Citation

Proteomics. 2010 Mar;10(5):1087-90.
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data.
Barsnes H, Eidhammer I, Martens L.