mmsearch: a motif arrangement language and search program.

This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins. AVAILABILITY: The program can be tested online at http://hits.isb-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz CONTACT: Thomas.Junier@isrec.unil.ch SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.     

Poxvirus Orthologous Clusters (POCs)

Poxvirus Orthologous Clusters (POCs) is a JAVA client-server application which accesses an updated database containing all complete poxvirus genomes; it automatically groups orthologous genes into families based on BLASTP scores for assessment by a human database curator. POCs has a user-friendly interface permitting complex SQL queries to retrieve interesting groups of DNA and protein sequences as well as gene families for subsequent interrogation by a variety of integrated tools: BLASTP, BLASTX, TBLASTN, Jalview (multiple alignment), Dotlet (Dotplot), Laj (local alignment), and NAP (nucleotide to amino acid alignment).     

PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences

Summary : An interactive dotmatrix program for the MacOS was designed that allows comparison of DNA to protein sequences using nested 3-frame translations. Availability : Shareware, available at http://copan.bioz.unibas.ch/software/ Contact : burglin@ubaclu. unibas.ch      

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

MOTIVATION: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer. AVAILABILITY: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL. CONTACT: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch.     

Computational cluster validation in post-genomic data analysis

MOTIVATION: The discovery of novel biological knowledge from the ab initio analysis of post-genomic data relies upon the use of unsupervised processing methods, in particular clustering techniques. Much recent research in bioinformatics has therefore been focused on the transfer of clustering methods introduced in other scientific fields and on the development of novel algorithms specifically designed to tackle the challenges posed by post-genomic data. The partitions returned by a clustering algorithm are commonly validated using visual inspection and concordance with prior biological knowledge--whether the clusters actually correspond to the real structure in the data is somewhat less frequently considered. Suitable computational cluster validation techniques are available in the general data-mining literature, but have been given only a fraction of the same attention in bioinformatics. RESULTS: This review paper aims to familiarize the reader with the battery of techniques available for the validation of clustering results, with a particular focus on their application to post-genomic data analysis. Synthetic and real biological datasets are used to demonstrate the benefits, and also some of the perils, of analytical clustervalidation. AVAILABILITY: The software used in the experiments is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/. SUPPLEMENTARY INFORMATION: Enlarged colour plots are provided in the Supplementary Material, which is available at http://dbkweb.ch.umist.ac.uk/handl/clustervalidation/.     

Quality estimation of multiple sequence alignments by Bayesian hypothesis testing

In this work we present a web-based tool for estimating multiple alignment quality using Bayesian hypothesis testing. The proposed method is very simple, easily implemented and not time consuming with a linear complexity. We evaluated method against a series of different alignments (a set of random and biologically derived alignments) and compared the results with tools based on classical statistical methods (such as sFFT and csFFT). Taking correlation coefficient as an objective criterion of the true quality, we found that Bayesian hypothesis testing performed better on average than the classical methods we tested. This approach may be used independently or as a component of any tool in computational biology which is based on the statistical estimation of alignment quality. AVAILABILITY: http://www.fmi.ch/groups/functional.genomics/tool.htm. SUPPLEMENTARY INFORMATION: Supplementary data are available from http://www.fmi.ch/groups/functional.genomics/tool-Supp.htm.     

Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis

SUMMARY: The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.     

L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes

SUMMARY: The Protein Ligand Database (PLD) is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/pld/     

The ENZYME database in 2000

The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/ ).     

FiRe and microarrays: a fast answer to burning questions

FiRe is a user-friendly Excel macro designed to survey microarray data rapidly. This software interactively assembles data from different experiments and produces lists of candidate genes according to patterns of gene expression. Furthermore, macros bundled with FiRe can compare lists of genes, merge information from different spreadsheets, link candidates to information available from web-based databases, and produce heat-maps for easy visualization of microarray data. FiRe is freely available at http://www.unifr.ch/plantbio/FiRe/main.html .     

Tracking current and forecasting future land-use impacts of agricultural value chains. 67th Discussion Forum on Life Cycle Assessment, 3rd of November 2017, Zurich,Switzerland

The 67th Discussion Forum on Life Cycle Assessment (LCA), organised by partners of the European project RELIEF (RELIability of product Environmental Footprints), focused on methods for better understanding the impacts of land use linked to agricultural value chains. The first session of the forum was dedicated to methods that help in retrospective tracking of land use within complex supply chains. Novel approaches were presented for the integration of increasingly available spatially located land use data into LCA. The second session focused on forward-looking projections of land use change and included emerging, predictive methods for the modelling of land change. The third session considered impact assessment methods related to the use of land and their application together with land change modelling approaches. Discussions throughout the day centred on opportunities and challenges arising from integrating spatially located land use information into Life Cycle Assessment. Increasing amounts of spatially located land use data are becoming available and this could potentially increase the robustness and specificity of Life Cycle Assessment. However, the use of such data can be computationally expensive and requires the development of skills (i.e. use of geographical information systems (GIS) and model coding) within the LCA community. Land change modelling and ecosystem service modelling are associated with considerable uncertainty which must be communicated appropriately to stakeholders and decision-makers when interpreting results from an LCA. The new approaches were found to challenge aspects of the traditional LCA approach—particularly the division between the life cycle inventory and impact assessment and the assumption of linearity between scale and impacts when deriving characterisation factors. The presentations from the DF-67 are available for download (www.lcaforum.ch), and video recordings can be accessed online (http://www.video.ethz.ch/events/lca/2017/autumn/67th.html).     

MACiE: a database of enzyme reaction mechanisms

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.     

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines. AVAILABILITY: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/.     

Phylogenetic reconstruction from non-genomic data

MOTIVATION: Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic pathways for several species makes it of greater relevance to understand the similarities and differences among such pathways. These similarities can then be used to infer phylogenetic trees not based exclusively in sequence data, therefore avoiding the previously mentioned problems. RESULTS: In this article, we present a method to assess the structural similarity of metabolic pathways for several organisms. Our algorithms work by using one of the three possible enzyme similarity measures (hierarchical, information content, gene ontology), and one of the two clustering methods (neighbor-joining, unweighted pair group method with arithmetic mean), to produce a phylogenetic tree both in Newick and graphic format. The web server implementing our algorithms is optimized to answer queries in linear time. AVAILABILITY: The software is available for free public use on a web server, at the address http://www.jaist.ac.jp/~clemente/cgi-bin/phylo.pl. It is available on demand in source code form for research use to educational institutions, non-profit research institutes, government research laboratories and individuals, for non-exclusive use, without the right of the licensee to further redistribute the source code.     

hierfstat,a package for r to compute and test hierarchical F‐statistics

The package hierfstat for the statistical software r , created by the R Development Core Team, allows the estimate of hierarchical F‐statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood‐ratio test. The package hierfstat is available at http://www.unil.ch/popgen/softwares/hierfstat.htm .     

Rgtsp: a generalized top scoring pairs package for class prediction

SUMMARY: A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance. AVAILABILITY AND IMPLEMENTATION: Full C++ source code and R package Rgtsp are freely available from http://lausanne.isb-sib.ch/~vpopovic/research/. The implementation relies on existing OpenMP libraries.     

Darwin v. 2.0: an interpreted computer language for the biosciences

MOTIVATION: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. RESULTS: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs. AVAILABILITY: Darwin is made available for most operating systems free of char ge from the Computational Biochemistry Research Group (CBRG), reachable at http://chrg.inf.ethz.ch. CONTACT: darwin@inf.ethz.ch     

Boosting for tumor classification with gene expression data

MOTIVATION: Microarray experiments generate large datasets with expression values for thousands of genes but not more than a few dozens of samples. Accurate supervised classification of tissue samples in such high-dimensional problems is difficult but often crucial for successful diagnosis and treatment. A promising way to meet this challenge is by using boosting in conjunction with decision trees. RESULTS: We demonstrate that the generic boosting algorithm needs some modification to become an accurate classifier in the context of gene expression data. In particular, we present a feature preselection method, a more robust boosting procedure and a new approach for multi-categorical problems. This allows for slight to drastic increase in performance and yields competitive results on several publicly available datasets. AVAILABILITY: Software for the modified boosting algorithms as well as for decision trees is available for free in R at http://stat.ethz.ch/~dettling/boosting.html.     

Changes in glucose and fructose level inNicotiana alata styles and ovaries accompanying compatible and incompatible pollen tube growth

Jestli?e byly pokusně květy den p?ed opylenim odděleny od rostliny a inkubovány ve vodě za teploty 25° C, projevil se v jejich pestících během následujících t?í dn? r?st pylových lá?ek v hladině glukosy a fruktosy. Prvý den po opylení bylo mno?ství těchto cukr? v apikálních ?ástech ?nělek z neopylených květ? vy??í, v basálních úsecích a v semeníeích naopak vět?inou ni??í ne? v p?íslu?ných ?ástech květ? opylených. V dal?ích dvou dnech do?lo i zde v p?ípadě opylení, a to p?edev?ím po allogamii, k silněj?ímu úbytku obou glycid?, tak?e po t?etím dnu bylo glukosy a fruktosy nejvíce v pestících neopylených, nejmáně po kompatibilním sprá?ení. Tento pokles byl nejvýrazněj?í v semeníeích, i kdy? do nich ani kompatibilní lá?ky je?tě nepronikly. V pokusech, kdy byly květy ponechány na rostlinách kultivovaných v polních podmínkách, nedo?lo v jejich pestících ani 80 hodin po kompatibilním opylení ke sní?ení obsahu glukosy a fruktosy. Z uvedených skute?ností lze vyvodit tyto záváry: R?st lá?ek ?nělkou vyvolá vá zvý?ený p?ísun glycid? do celých pestík?. Jak kompatibilní, tak inkompatibilní lá?ky vyu?ívají cukry z ?nělkováho pletiva. Oba tyto jevy jsou intenzívněj?í po allogamii ne? v p?ípadě inkompatibilní autogamie. Vzhledem k tomu, ?e kompatibilní lá?ky rostly normálně ?nělkou i za sní?ené hladiny glukosy a fruktosy, není absolutní zvý?ení obsahu těchto cukr? v pestících pro r? st lá?ek nezbytné. V opylených ?nělkách se mění poměr glukosa/fruktosa ve prospěch glukosy. Hodnota tohoto kvocientu se zvy?uje jak v apikálních, tak v basálních ?ásteeh ?ně1ek p?edev?ím po opylení kompatibilním. Tento jev je v souladu s hypothesou uvedenou d?ive (TUpý- 1959, 1960 podle ní? pylové lá?ky prodýchávají hlavnð sacharosu a z ní p?edev?ím její fruktofuranosovou slo?ku.