PD5 1.5 – Software Library for the Development of Primer Design Applications

PD5 1.5

:: DESCRIPTION

PD5 is a C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

PD5 Online Version

::DEVELOPER

the Bioinformatics group in the Department of Computer Science at Aberystwyth University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOSX / Linux
C++ Compiler

:: DOWNLOAD

PD5

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e80156. doi: 10.1371/journal.pone.0080156.
PD5: A General Purpose Library for Primer Design Software.
Riley MC, Aubrey W, Young M, Clare A.

BiSSAP 1.3 – Biological Sequence Submission Application for Patents

BiSSAP 1.3

:: DESCRIPTION

BiSSAP is a computer program designed to facilitate the creation of sequence listings for patent applications containing biological sequences (see Rule 30 EPC, Rule 5.2 PCT, and the Decision of the President and Notice from the EPO dated 28 April 2011 (OJ EPO 6/2011, 372 ff.)).

::DEVELOPER

EPO BiSSAP Team (bissap@epo.org)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

BiSSAP

:: MORE INFORMATION

BioCRF 0.9 – Grammatical-Restrained HCRF tool for Bioinformatics applications

BioCRF 0.9

:: DESCRIPTION

BioCRF is an implementation of Grammatical-Restrained Hidden Conditional Random Fields (GRHCRFs) , an extension of linear HCRF to include prior knowledge about the problem at hand by means of a regular grammar. This results very useful in several Bioinformatics problems where only solution that agree with a regular grammar rules are biologically meaningful.

::DEVELOPER

Castrense Savojardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
C++ Compiler

:: DOWNLOAD

BioCRF

:: MORE INFORMATION

Citation

Piero Fariselli, Castrense Savojardo, Pier L Martelli and Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications
Algorithms for Molecular Biology 2009, 4:13

Pebble 1.0 – Phylogenetic Analysis Application

Pebble 1.0

:: DESCRIPTION

Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a powerful application for Phylogenetic analysis. The primary purpose of Pebble is to provide tools for analysis and simulation of serially sampled sequence data (through maximum likelihood, and least-squares methods). Implemented forms of simulation include: trees, via a coalescent model, and sequence alignments, given an input tree and substitution model. Extra functionality includes data manipulation tools for sequence alignments and phylogenetic trees, as well as useful inbuilt alignment construction and editing facilities.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

Pebble

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2004 May;Chapter 6:Unit 6.8. doi: 10.1002/0471250953.bi0608s05.
Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.
Goode M, Rodrigo AG.

FUNC 0.4.9 – Gene Analyzer Application

FUNC 0.4.9

:: DESCRIPTION

FUNC is a collection of four programs to analyze the over- and under-representation of data associated with genes or gene products. The test runs seperately for all three taxonomies of Gene Ontology (or the supplied root-nodes).

::DEVELOPER

Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R package

:: DOWNLOAD

FUNC

:: MORE INFORMATION

Citation

Kay Prüfer et al.
FUNC: a package for detecting significant associations between gene sets and ontological annotations.
BMC Bioinformatics. 2007 Feb 6;8:41.

Bio-SeCo – Bioinformatics Search Computing Application

Bio-SeCo

:: DESCRIPTION

Bio-SeCo allows exploring and integrating data from external resources (e.g. NCBI and WU BLAST, Array Express, …).

::DEVELOPER

Bio-SeCo team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 1:S3. doi: 10.1186/1471-2105-15-S1-S3. Epub 2014 Jan 10.
Explorative search of distributed bio-data to answer complex biomedical questions.
Masseroli M, Picozzi M, Ghisalberti G, Ceri S.

Disperse 1.0.3 – Design of Selector Assays for Targeted Resequencing Applications

Disperse 1.0.3

:: DESCRIPTION

The Disperse project aims to develop and distribute software and data for design of selector assays for exon resequencing applications. The software consists of Java and Perl code integrated into a pipeline that performs all tasks required to transform a list of gene names to a set of selector probes targetting all exonic regions of those genes

::DEVELOPER

Disperse Team

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows / Linux
Java
Perl
Blast

:: DOWNLOAD

Disperse

:: MORE INFORMATION

Citation

J. Stenberg, M. Zhang and H. Ji
Disperse–a software system for design of selector probes for exon resequencing applications
Bioinformatics (2009) 25(5): 666-667

ChemDoodle 11.6 – Chemical Drawing Application

ChemDoodle 11.6

:: DESCRIPTION

ChemDoodle is a fully functional chemical drawing application!ChemDoodle also natively reads and writes many common file formats including ChemDraw’s CDX and CDXML. You can write ChemDraw files for submitting journal manuscripts or share these files with your rich friends who purchased ChemDraw. No longer do you need to worry if your colleages are using compatible applications or operating systems.

::DEVELOPER

iChemLabs

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX / IOS/ Andorid
Java

:: DOWNLOAD

ChemDoodle free trial

:: MORE INFORMATION

ClassifyR 2.12.0 – Performance Assessment of Classification with Applications to Transcriptomics

ClassifyR 2.12.0

:: DESCRIPTION

ClassifyR is a framework for two-class classification problems, with applications to differential variability and differential distribution testing.

::DEVELOPER

Dario Strbenac <dario.strbenac at sydney.edu.au>, John Ormerod, Graham Mann, Jean Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
BioConductor

:: DOWNLOAD

ClassifyR

:: MORE INFORMATION

Citation

ClassifyR: An R Package for Performance Assessment of Classification with Applications to Transcriptomics.
Strbenac D, Mann GJ, Ormerod JT, Yang JY.
Bioinformatics. 2015 Feb 1. pii: btv066.

GenSkew – Genomic Nucleotide Skew Application

GenSkew

:: DESCRIPTION

GenSkew is an application for computing and plotting nucleotide skew data.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

GenSkew

:: MORE INFORMATION