This paper builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool to encode and to represent such motions. We investigate several applications and show results that illustrate the interest of such representation. (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)

Summary: ArchSchema is a Java Web Start application that generates a dynamic 2D network of related Pfam domain architectures. Each node corresponds to a different architecture (shown as a sequence of coloured boxes) and indicates whether any 3D structural information is available in the PDB. Satellite nodes can show either the UniProt codes or the PDB codes of proteins having the given architecture. Search options allow search by UniProt code or Pfam domain identifier, and results can be filtered by domain, organism, or by selecting only proteins in the PDB.
Availability: ArchSchema can be freely accessed at http://www.ebi.ac.uk/Tools/archschema
Contact: roman@ebi.ac.uk (Source: Bioinformatics)

Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision and sampling density. This generates large amounts of data for the analysis of which computer tools are missing to date.
Results: We have developed WellReader, a MATLAB program for the analysis of fluorescent and luminescent reporter gene data. WellReader allows the user to load the output files of microplate readers, remove outliers, correct for background effects and smooth and fit the data. Moreover, it computes biologically relevant quantities from the measured signals, notably promoter activities and protein concentrations, and compares the resulting expression profiles of different genes …

Summary: Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives. Such transcript half-lives provide important insights into the regulation of biological processes and the relative contributions of RNA decay and de novo transcription to differential gene expression. In this article, we present HALO (Half-life Organizer), the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command-line tools and a well-documented Ja…

Summary: Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. The Confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. The database includes the gene modules for Arabidopsis thaliana (thale cress) and seven crops, Glycine max (soybean), Hordeum vulgare (barley), Oryza sativa (rice), Populus trichocarpa (poplar), Triticum aestivum (wheat), Vitis vinifera (grape) and Zea mays (maize).
Availability: The CoP database is available at: http://…

Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studies (GWAS). However, such inter-population LD differences can be leveraged to narrow the search for common causal variants responsible for the association signals observed. The ability to assess and quantify LD variations among populations is thus expected to contribute to both replication and fine-mapping stages of GWAS.
Availability: The program varLD is available for download from http://www.nus-cme.org.sg/software/varld.html
Contact: statyy@nus.edu.sg (Source: Bioinformatics)

Summary: TopoGSA (Topology-based Gene Set Analysis) is a web-application dedicated to the computation and visualization of network topological properties for gene and protein sets in molecular interaction networks. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, can be computed and compared with those of known cellular pathways and processes.
Availability: Freely available at http://www.infobiotics.net/topogsa
Contact: nxk@cs.nott.ac.uk; avalencia@cnio.es (Source: Bioinformatics)

In this study, a statistical method is introduced to detect tissue-specific genes from more than 123 125 gene expression profiles over 107 human tissues, 67 mouse tissues and 30 rat tissues. As a result, a novel subject-specialized repository, namely the tissue-specific genes database (TiSGeD), is developed to represent the analyzed results. Auxiliary information of tissue-specific genes was also collected from biomedical literatures.
Availability: http://bioinf.xmu.edu.cn/databases/TiSGeD/index.html
Contact: appo@bioinf.xmu.edu.cn; zhiliang.ji@gmail.com (Source: Bioinformatics)

Conclusions: For sparse contingency tables of the type universally observed in protein coevolution studies, our results show that estimates of MI, and hence inferences about physical phenomena such as coevolution, are critically dependent on at least three prior assumptions. These assumptions are: (i) how observation counts relate to expected frequencies; (ii) the relationship between joint and marginal frequencies; and (iii) how non-observed categories are interpreted. In any biologically relevant data, these assumptions will affect the MI estimate as much or more-so than observed data, and are independent of uncertainty in frequency parameters.
Contact: andrew@fernandes.org
Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)

We describe here LOTUS, a hitherto uncharacterized small globular domain, which was identified using sensitive sequence profile analysis. The LOTUS domain is found in germline-specific proteins that are present in the nuage/polar granules of germ cells. TDRD5 and TDRD7, two mammalian members of the germline Tudor group, possess three copies of the LOTUS domain in their extreme N-termini. The Tudor domains of these proteins bind symmetric dimethyl arginines present on the germ cell-specific Piwi proteins, which form a particular clade of Argonaute proteins. Piwi proteins interact with a specific class of non-coding RNAs [piwi-interacting RNAs (piRNAs)] and play a key role in the repression (silencing) of transposons and possibly other germline-specific functions. A LOTUS domain is also pres…