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.

HTSeq 0.6.1 – Process and Analyze data from High-throughput Sequencing (HTS) Assays

HTSeq 0.6.1

:: DESCRIPTION

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

::DEVELOPER

Simon Anders at EMBL Heidelberg (Genome Biology Unit)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HTSeq

:: MORE INFORMATION

Citation

HTSeq–a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W.
Bioinformatics. 2015 Jan 15;31(2):166-9. doi: 10.1093/bioinformatics/btu638.

BALM 1.0.1 – Analyze MBD-seq

BALM 1.0.1

:: DESCRIPTION

BALM ( bi-asymmetric-Laplace model) was developed to analyze MBD-seq. We compared the resolution of BALM to that of several ChIP-seq analysis tools. The results demonstrate the program’s superior ability to distinguish methylation statuses of closely positioned CpG sites. This study demonstrates that MBD-seq combined with the new program is potentially a powerful tool to capture genome-wide DNA methylation profiles with high efficiency and resolution.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

BALM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  BALM

:: MORE INFORMATION

Citation

Lan X, Adams C, Landers M, Dudas M, Krissinger D, et al. (2011)
High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBDSeq Technology.
PLoS ONE 6(7): e22226. doi:10.1371/journal.pone.0022226

Trans-ABySS 1.5.3 – Analyze ABySS multi-k-assembled Shotgun Transcriptome Data.

Trans-ABySS 1.5.3

:: DESCRIPTION

Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a much smaller set of nonredundant contigs. It contains scripts that map assembled contigs to known transcripts, currently supporting Blat and Exonerate contig-to-genome aligners. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also estimate gene expression levels, identify candidate polyadenylation sites, and identify candidate gene-fusion events.

::DEVELOPER

Readman Chiu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Trans-ABySS

:: MORE INFORMATION

Citation

Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I.
De novo assembly and analysis of RNA-seq data.
Nat Methods. 2010 Nov;7(11):909-12. Epub 2010 Oct 10.

STAMP 2.1.3 – Analyze Metagenomic Profiles

STAMP 2.1.3

:: DESCRIPTION

STAMP (Statistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation

STAMP: statistical analysis of taxonomic and functional profiles.
Parks DH, Tyson GW, Hugenholtz P, Beiko RG.
Bioinformatics. 2014 Jul 23. pii: btu494.

Parks, D.H. and Beiko, R.G. (2010).
Identifying biologically relevant differences between metagenomic communities.
Bioinformatics, 26, 715-721.

DisGeNET 3.0 – Query and Analyze a Network representation of human Gene-disease databases

DisGeNET 3.0

:: DESCRIPTION

DisGeNET is a plugin for Cytoscape to query and analyze a network representation of human gene-disease databases. For this purpose, we have developed a new gene-disease database integrating data from several public sources. DisGeNET allows user-friendly access to our database, which includes queries restricted to (i) the original data source, (ii) the association type, (iii) the disorder class of interest and (iv) specific diseases, respectively genes. It represents gene-disease associations in terms of bipartite graphs and additionally provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Moreover, DisGeNET permits multicoloring of nodes (genes/diseases) according to their disease classes for expedient visualization

::DEVELOPER

The Integrative Biomedical Informatics group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  DisGeNET

:: MORE INFORMATION

Citation

Anna Bauer-Mehren; Michael Rautschka; Ferran Sanz; Laura I. Furlong:
DisGeNET – a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.
Bioinformatics, Vol. 26, No. 22. (15 November 2010), pp. 2924-2926.

FragmentationAnalyzer 1.5.13 – Analyze MS/MS Fragmentation Data

FragmentationAnalyzer 1.5.13

:: 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.

PhylochipAnalyzer 1.0 – Analyse Hierarchical Probe sets

PhylochipAnalyzer 1.0

:: DESCRIPTION

PhylochipAnalyzer is a Windows-program for the analysis of experiments with hierarchical probe-sets. It operates in two modes: first, the hierarchy of probes is defined interactively, second, the intensity data of a hybridized chip is loaded and analyzed according to the hierarchy. The program can export hierarchy trees to Newick-format and analyzed data to Excel. It contains a Delphi-script that makes it configurable with respect to different criteria for positive signals.

::DEVELOPER

PhylochipAnalyzer team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PhylochipAnalyzer

:: MORE INFORMATION

Citation:

Metfies K, Borsutzki P, Gescher C, Medlin LK, Frickenhaus S
Phylochipanalyser — a program for analysing hierarchical probe sets
Molecular Ecology Resources (2008) 8, 99–102
doi:10.1111/j.1471-8286.2007.01927.x