SHORE 0.9.3 – Analysis Suite for Illumina Short Read Data

SHORE 0.9.3

:: DESCRIPTION

SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHORE

:: MORE INFORMATION

Citation

Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

Utopia 1.4.5 – Protein Analysis Suite

Utopia 1.4.5

:: DESCRIPTION

Utopia (User-friendly Tools for OPerating Informatics Applications) is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services. It hides the representation of the protein data and analysis tools from users. Instead users are able to interact with the data in terms appropriate to the domain of protein analysis rather than program algorithms and data.

::DEVELOPER

The University of Manchester

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OS X / Windows

:: DOWNLOAD

Utopia

:: MORE INFORMATION

Citation

J.R.Sinnott,; T.K.Attwood,S.Pettifer,
UTOPIA: user friendly tools for operating informatics applications
Comparative and Functional Genomics, JAN, Volume 5, p.56-60, (2004)

S. Pettifer, K. Wolstencroft, P. Alper, T. Attwood A. Coletta, C. Goble, P. Li, P. McDermott, J. Marsh, T. Oinn, J. Sinnott and D. Thorne
myGrid and UTOPIA: an Integrated Approach To Enacting And Visualising In Silico Experiments in the Life Sciences
Lecture Notes in Bioinformatics (2007)

Babelomics 5 – Gene Expression and Functional Profiling Analysis Suite

Babelomics 5

:: DESCRIPTION

Babelomics is a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available.

::DEVELOPER

Bioinformatics and Genomics Department at CIPF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  No, Only Web Service

:: MORE INFORMATION

Citation

Babelomics 5.0: functional interpretation for new generations of genomic data.
Alonso R, Salavert F, Garcia-Garcia F, Carbonell-Caballero J, Bleda M, Garcia-Alonso L, Sanchis-Juan A, Perez-Gil D, Marin-Garcia P, Sanchez R, Cubuk C, Hidalgo MR, Amadoz A, Hernansaiz-Ballesteros RD, Alemán A, Tarraga J, Montaner D, Medina I, Dopazo J.
Nucleic Acids Res. 2015 Apr 20. pii: gkv384

Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J.
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W210-3. Epub 2010 May 16.

LOHAS 2.1 – Loss-of-heterozygosity Analysis Suite

LOHAS 2.1

:: DESCRIPTION

LOHAS (Loss-Of-Heterozygosity Analysis Suite) written in R and R GUI is developed to estimating homozygous intensity, identifying samples with unusual genomes, clustering samples with close LOH structures, and mapping the genomic segments bearing LOH by analyzing data of genome-wide SNP arrays or customized SNP arrays. In addition to cancer genetics and cancer genomics, LOHAS can also be applied to study long contiguous stretches of homozygosity (LCSH) in general populations. The LCSH analysis aids to identify samples with complex LCSH patterns, separate samples with different genetic background and gender in genetics, and locate LCSH regions.

::DEVELOPER

Hsin-Chou Yang

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 LOHAS

:: MORE INFORMATION

Citation

Yang, H.-C., Chang, L.-C., Huggins, R. M., Chen, C.-H. and Mullighan, C. G. (2011/05).
LOHAS: Loss-of-heterozygosity analysis suite.
Genetic Epidemiology 35, 247-260

PBM – Universal Protein Binding Microarray Analysis Suite

PBM

:: DESCRIPTION

PBM Analysis Suite provides the in-house tools and the procedural methods used in the analysis of universal protein binding microarrays (PBMs) synthesized by Agilent Techonologies

::DEVELOPER

The Bulyk Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl

:: DOWNLOAD

 PBM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1390-8. doi: 10.1093/bioinformatics/btt152. Epub 2013 Apr 4.
Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.
Jiang B1, Liu JS, Bulyk ML.

Berger MF, ML Bulyk
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.
Nature Protocols. (2009) 4(3):393-411