Tag: Analyze

ChromatoGate 1.2 – Analyze / Edit Chromatogram data

ChromatoGate 1.2

:: DESCRIPTION

ChromatoGate (CG) has been created to accelerate the process of detecting possible errors in DNA sequences that have been introduced by Sanger sequencers. To detect possible errors in the sequences, CG starts from the multiple-sequence alignment instead of inspecting every sequence separately.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ChromatoGate

:: MORE INFORMATION

Citation

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection
Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis
7th conference of the Hellenic Society for Computational Biology and Bioinformatics Volume No: 6, Issue: 7, March 2013, e201303001,

PrimerProspector 1.0.1 – Design and Analyze PCR Primers

PrimerProspector 1.0.1

:: DESCRIPTION

PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • PyCogent
  • Numpy
  • Matplotlib

:: DOWNLOAD

 PrimerProspector

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1159-61. doi: 10.1093/bioinformatics/btr087.
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers.
Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R.

PCS 1.5 – Identify and Analyze Conserved K-mers in Pairwise Alignment

PCS 1.5

:: DESCRIPTION

PCS (Pairwise Conservation Scores) is stand-alone pakage to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3′-UTRs.

::DEVELOPER

Bioinformatics & Intelligent Information Processing Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Perl 

:: DOWNLOAD

 PCS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Nov 8;8:432.
Identifications of conserved 7-mers in 3′-UTRs and microRNAs in Drosophila.
Gu J, Fu H, Zhang X, Li Y.

vtools 3.0.4 – Annotate, Summarize and Analyze Next-gen Sequencing Variation data

vtools 3.0.4

:: DESCRIPTION

vtools (variant tools) is a set of tools for annotating and tracking sequence variation for large-scale exome sequencing projects. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C++ compiler
  • Python

:: DOWNLOAD

 vtools

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):421-2. Epub 2011 Dec 2.
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
San Lucas FA, Wang G, Scheet P, Peng B.

YANAsquare 201212 / YANAvergence – Integrated Network Reconstruction, Visualization and Analysis

YANAsquare 201212 / YANAvergence

:: DESCRIPTION

YANA has been upgraded and replaced by his successor, YANAsquare software package

YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.

YANAvergence is an important extension to YANAsquare software, which allows integrating more expermental data to inspect the adaptation of metabolic network under different stresses, conditions.

::DEVELOPER

LEHRSTUHL FüR BIOINFORMATIK, University of Würzburg, Germany

:: SCREENSHOTS

YANAsquare

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java
  • R package

:: DOWNLOAD

 YANAsquare/ YANAvergence

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 Jun 1;6:135.
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities.
Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T.

BMC Bioinformatics. 2007 Aug 28;8:313.
Integrated network reconstruction, visualization and analysis using YANAsquare.
Schwarz R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T.

GeneTalk – Analyze Human Sequence Variants

GeneTalk

:: DESCRIPTION

GeneTalk is a web-based platform that serves as an expert exchange network for the assessment of personal and potentially disease-relevant sequence variants. GeneTalk assists a clinical geneticist who is searching for information about specific sequence variants and connects this user to other users with expertise for the same sequence variant.

::DEVELOPER

GeneTalk team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 1;28(19):2515-6. Epub 2012 Jul 23.
GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes.
Kamphans T, Krawitz PM.

GEM library PR3 – Index/Analyze Huge Genomes

GEM library PR3

:: DESCRIPTION

GEM Library  (GEnome Multi-tool)  is a set of very optimized tools for indexing/querying huge genomes/files. Provided so far are a very fast exhaustive mapper (the GEM mapper), an unconstrained split mapper (the GEM split mapper), and a very fast program to compute genome mappability (the GEM mappability).

::DEVELOPER

GEM library Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GEM library

:: MORE INFORMATION

Swiss-PdbViewer 4.1 – Analyze Several Proteins 3D Structure at the Same Time

Swiss-PdbViewer 4.1

:: DESCRIPTION

DeepView (Swiss-PdbViewer) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

::DEVELOPER

the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

DeepView

:: MORE INFORMATION

Citation:

Guex, N. and Peitsch, M.C. (1997)
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling.
Electrophoresis 18, 2714-2723.

Epi-Speller – Analyze Multiple Genome-wide Profiling Epigenomic data

Epi-Speller

:: DESCRIPTION

Epi-Speller is a program for analyzing multiple genome-wide profiling epigenomic data.

::DEVELOPER

Huy Q. Dinh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • C++ Compiler
  • Perl

:: DOWNLOAD

 Epi-Speller

:: MORE INFORMATION

Citation

Dinh HQ, Mittelsten Scheid O, von Haeseler A.
Epi-Speller – a bioinformatic tool for epigenomic signature discovery.
submitted.

 

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