OTUbase: an R infrastructure package for operational taxonomic unit data

SUMMARY: OTUbase is an R package designed to facilitate the analysis of operational taxonomic unit (OTU) data and sequence classification (taxonomic) data. Currently there are programs that will cluster sequence data into OTUs and/or classify sequence data into known taxonomies. However, there is a need for software that can take the summarized output of these programs and organize it into easily accessed and manipulated formats. OTUbase provides this structure and organization within R, to allow researchers to easily manipulate the data with the rich library of R packages currently available for additional analysis. AVAILABILITY: OTUbase is an R package available through Bioconductor. It can be found at http://www.bioconductor.org/packages/release/bioc/html/OTUbase.html.     

GenomeDiagram: a python package for the visualization of large-scale genomic data

SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. AVAILABILITY: GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.     

HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations

SUMMARY: Understanding of human variation relevant to association studies can benefit from population comparison, especially comparing populations in the same geographical region. Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern. We present here a win32 system based Perl/Tk application for visual comparisons of these variations in different populations. AVAILABILITY: The application package is available at http://info.med.yale.edu/genetics/kkidd/programs.html CONTACT: sheng.gu@yale.edu.     

Drawing phylogenetic trees in LATEX and Microsoft Word

SUMMARY: newicktree is a PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. mswordtree is a macro for producing phylogenetic trees using the drawing elements available in Microsoft Word. AVAILABILITY: Both programs are available free from the John Innes Centre's Bioinformatics Research Group website at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html. SUPPLEMENTARY INFORMATION: A full user-guide for newicktree and installation and usage instructions for mswordtree and available at http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/software/index.html     

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments

SUMMARY: As was shown in Nagarajan et al. (2005), commonly used approximations for assessing the significance of multiple alignments can be be very inaccurate. To address this, we present here the FAST package, an open-source collection of programs and libraries for efficiently and reliably computing the significance of ungapped local alignments. We also describe other potential applications in Bioinformatics where these programs can be adapted for significance testing. AVAILABILITY: The FAST package includes C++ implementations of various algorithms that can be used as stand-alone programs or as a library of subroutines. The package and a web-server for some of the programs are available at www.cs.cornell.edu/~keich/FAST.     

Implementation of a gene expression index calculation method based on the PDNN model

SUMMARY: Gene expression index calculations from Affymetrix GeneChips have been dominated by the Affymetrix MAS, dChip, and RMA methods. A new method to estimate the gene expression value utilizing the probe sequence information named position-dependent nearest-neighbor (PDNN) has been suggested by Zhang et al. (2003). Here we describe an open source implementation of the PDNN method for the statistical language R. AVAILABILITY: The package can be downloaded from http://www.bioconductor.org/repository/devel/package/html/affypdnn.html CONTACT: hbjorn@cbs.dtu.dk.     

ontoCAT: an R package for ontology traversal and search

MOTIVATION: There exist few simple and easily accessible methods to integrate ontologies programmatically in the R environment. We present ontoCAT-an R package to access ontologies in widely used standard formats, stored locally in the filesystem or available online. The ontoCAT package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories. AVAILABILITY: The package and sources are freely available in Bioconductor starting from version 2.8: http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html or via the OntoCAT website http://www.ontocat.org/wiki/r. CONTACT: natalja@ebi.ac.uk; natalja@ebi.ac.uk.     

Electrophoretic data classification for phylogenetics and biostatistics

SUMMARY: This paper presents ClassMaker, a macro of MS Excel able to classify continuous data of molecular weight data as binary (1/0) values. The output is represented by a binary matrix, which can be introduced in every software application for phylogenetics or multivariate statistics. This application is designed in order to be a link between image analysis programs and statistical or phylogenetic applications, in order to produce a complete series of free programs able to carry out the complete analysis from the gel to the dendrogram. AVAILABILITY: ClassMaker is freely available from http://www.agr.unipg.it/cardinali/index.html, where a list of the URLs from which programs of image analysis, statistics and phylogenetics can be freely downloaded.     

Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles

SUMMARY: If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called 'Clonality'. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results. AVAILABILITY: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.     

Apple Macintosh programs for nucleic and protein sequence analyses

This paper describes a package of programs for handling and analyzing nucleic acid and protein sequences using the Apple Macintosh microcomputer. There are three important features of these programs: first, because of the now classical Macintosh interface the programs can be easily used by persons with little or no computer experience. Second, it is possible to save all the data, written in an editable scrolling text window or drawn in a graphic window, as files that can be directly used either as word processing documents or as picture documents. Third, sequences can be easily exchanged with any other computer. The package is composed of thirteen programs, written in Pascal programming language.     

phangorn: phylogenetic analysis in R

SUMMARY: phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. AVAILABILITY: phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.     

snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package

snp.plotter is a newly developed R package which produces high-quality plots of results from genetic association studies. The main features of the package include options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D' LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme. snp.plotter can plot single SNP and/or haplotype data and simultaneously plot multiple sets of results. R is a free software environment for statistical computing and graphics available for most platforms. The proposed package provides a simple way to convey both association and LD information in a single appealing graphic for genetic association studies. AVAILABILITY: Downloadable R package and example datasets are available at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html and http://www.r-project.org.     

Mfuzz: a software package for soft clustering of microarray data

For the analysis of microarray data, clustering techniques are frequently used. Most of such methods are based on hard clustering of data wherein one gene (or sample) is assigned to exactly one cluster. Hard clustering, however, suffers from several drawbacks such as sensitivity to noise and information loss. In contrast, soft clustering methods can assign a gene to several clusters. They can overcome shortcomings of conventional hard clustering techniques and offer further advantages. Thus, we constructed an R package termed Mfuzz implementing soft clustering tools for microarray data analysis. The additional package Mfuzzgui provides a convenient TclTk based graphical user interface. AVAILABILITY: The R package Mfuzz and Mfuzzgui are available at http://itb1.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/index.html. Their distribution is subject to GPL version 2 license.     

EXP-PAC: providing comparative analysis and storage of next generation gene expression data

Microarrays and more recently RNA sequencing has led to an increase in available gene expression data. How to manage and store this data is becoming a key issue. In response we have developed EXP-PAC, a web based software package for storage, management and analysis of gene expression and sequence data. Unique to this package is SQL based querying of gene expression data sets, distributed normalization of raw gene expression data and analysis of gene expression data across experiments and species. This package has been populated with lactation data in the international milk genomic consortium web portal (http://milkgenomics.org/). Source code is also available which can be hosted on a Windows, Linux or Mac APACHE server connected to a private or public network (http://mamsap.it.deakin.edu.au/~pcc/Release/EXP_PAC.html).     

AStream: an R package for annotating LC/MS metabolomic data

AStream, an R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data, is described. AStream detects isotopic, fragment and adduct patterns by identifying feature pairs that fulfill expected relational patterns. Data reduction by AStream allows compounds to be identified reliably and subsequently linked to metabolite databases. AStream provides researchers with a fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing consistency of results. AVAILABILITY: The AStream R package and a study example can be freely accessed at http://www.urr.cat/AStream/AStream.html.     

Sequence search algorithm assessment and testing toolkit (SAT)

MOTIVATION: The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm. RESULTS: An analysis on two different data sets was carried out using the SAT package. It compared the performance of a full protein sequence database (RSDB100) with a non-redundant representative sequence database derived from it (RSDB50). The performance measurement indicated that the full database is sub-optimal for a homology search. This result justifies the use of much smaller and faster RSDB50 than RSDB100 for the SAT. AVAILABILITY: A web site is up. The whole packa ge is accessible via www and ftp. ftp://ftp.ebi.ac.uk/pub/contrib/jong/SAT http://cyrah.ebi.ac.uk:1111/Proj/Bio/SAT http://www.mrc-lmb.cam.ac.uk/genomes/SAT In the package, some previous assessment results produced by the package can also be found for reference. CONTACT: jong@ebi.ac.uk