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This page shows you the most recent publications within this specialty of the MedWorm directory. This is page number 39.

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Source: Computers in Biology and Medicine - April 5, 2012 Category: Bioinformatics Source Type: research

CLIPS-1D: Analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure
Conclusions: CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about residue-positions important for a set of homologous proteins and focuses on conservation and abundance signals. Thus, the algorithm can be applied in cases where function cannot be transferred from well-characterized proteins by means of sequence comparison.
Source: BMC Bioinformatics - Latest articles - April 5, 2012 Category: Bioinformatics Authors: Jan-Oliver JandaMarkus BuschFabian KuckMikhail PorfenenkoRainer Merkl Source Type: research

New Moment Closures Based on A Priori Distributions with Applications to Epidemic Dynamics.
Abstract Recently, research that focuses on the rigorous understanding of the relation between simulation and/or exact models on graphs and approximate counterparts has gained lots of momentum. This includes revisiting the performance of classic pairwise models with closures at the level of pairs and/or triples as well as effective-degree-type models and those based on the probability generating function formalism. In this paper, for a fully connected graph and the simple SIS (susceptible-infected-susceptible) epidemic model, a novel closure is introduced. This is done via using the equations for the moments of the...
Source: Bulletin of Mathematical Biology - April 4, 2012 Category: Bioinformatics Authors: Kiss IZ, Simon PL Tags: Bull Math Biol Source Type: research

Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm
Conclusions: Our analysis showed that OPTricluster generally outperforms other well known clustering algorithms such as the TRICLUSTER, gTRICLUSTER and K-means; it is robust to noise and can effectively mine the biological knowledge hidden in the 3D short time-series gene expression data.
Source: BMC Bioinformatics - Latest articles - April 4, 2012 Category: Bioinformatics Authors: Alain TchagangSieu PhanFazel FamiliHeather ShearerPierre FobertYi HuangJitao ZouDaiqing HuangAdrian CutlerZiying LiuYoulian Pan Source Type: research

Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control
Conclusions: Our final network contains 118 previously associated and novel genes affecting weight, cholesterol, glucose, and free fatty acid levels that are excellent obesity risk candidates.
Source: BMC Bioinformatics - Latest articles - April 2, 2012 Category: Bioinformatics Authors: Benjamin LogsdonGabriel HoffmanJason Mezey Source Type: research

Identification of shortened 3' untranslated regions from expression arrays.
We present here a computational procedure for systematically identifying shortened 3'UTRs by Affymetrix 3' microarrays. The advantage of this technology compared to more recent and promising ones such as exon arrays and RNA-Seq is that, giving the relatively small cost, already existing datasets in public databases include a considerably higher number of experiments. Moreover, the design of Affymetrix Gene Chips is well-suited for 3'UTR analysis of a large number of genes. Initially, Affymetrix individual probes are regrouped into customized probesets mapping specifically the CDS or the 3'UTR of the transcript, according t...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Martignetti L, Zinovyev A, Barillot E Tags: J Bioinform Comput Biol Source Type: research

Structure fluctuations and conformational changes in protein binding.
Abstract Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may unde...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Ruvinsky AM, Kirys T, Tuzikov AV, Vakser IA Tags: J Bioinform Comput Biol Source Type: research

SHEEP: A TOOL FOR DESCRIPTION OF β-SHEETS IN PROTEIN 3D STRUCTURES.
Abstract The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Aksianov E, Alexeevski A Tags: J Bioinform Comput Biol Source Type: research

Deppdb - DNA electrostatic potential properties database: electrostatic properties of genome DNA elements.
Abstract Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids geno...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Osypov AA, Krutinin GG, Krutinina EA, Kamzolova SG Tags: J Bioinform Comput Biol Source Type: research

Analysis of context-dependent errors for illumina sequencing.
Abstract The new generation of short-read sequencing technologies requires reliable measures of data quality. Such measures are especially important for variant calling. However, in the particular case of SNP calling, a great number of false-positive SNPs may be obtained. One needs to distinguish putative SNPs from sequencing or other errors. We found that not only the probability of sequencing errors (i.e. the quality value) is important to distinguish an FP-SNP but also the conditional probability of "correcting" this error (the "second best call" probability, conditional on that of the first call). Surprisingly,...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Abnizova I, Leonard S, Skelly T, Brown A, Jackson D, Gourtovaia M, Qi G, Te Boekhorst R, Faruque N, Lewis K, Cox T Tags: J Bioinform Comput Biol Source Type: research

Practicality and time complexity of a sparsified RNA folding algorithm.
Abstract Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n(3)). Recently, it has been claimed that RNA folding can be achieved in average time O(n(2)) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computational RNA folding obeys the "polymer-zeta property". Several variants of sparse RNA folding algorithms were later developed. Here, we present our own version, which is readily applicable to existing RNA folding progr...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Dimitrieva S, Bucher P Tags: J Bioinform Comput Biol Source Type: research

Derived SNP alleles are used more frequently than ancestral alleles as risk-associated variants in common human diseases.
Abstract Evolutionary aspects of the genetic architecture of common human diseases remain enigmatic. The results of more than 200 genome-wide association studies published to date were compiled in a catalog (). We used cataloged data to determine whether derived (mutant) alleles are associated with higher risk of human disease more frequently than ancestral alleles. We placed all allelic variants into ten categories of population frequency (0%-100%) in 10% increments. We then analyzed the relationship between allelic frequency, evolutionary status of the polymorphic site (ancestral versus derived), and disease risk...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Gorlova OY, Ying J, Amos CI, Spitz MR, Peng B, Gorlov IP Tags: J Bioinform Comput Biol Source Type: research

VirE2-DEPENDENT PORES FOR ssDNA TRANSFER ACROSS ARTIFICIAL AND CELL MEMBRANES.
Abstract The transfer of single-stranded (ss) T-DNA from soil bacteria of the genus Agrobacterium with the help of the VirE2 protein, which possibly mediates the delivery of ss-T-DNA across the cell membrane, was demonstrated earlier, but how VirE2 participates in ssDNA transfer across artificial and natural membranes is not known. Using computational methods, we reconstructed model structures composed of two and four VirE2 proteins and showed by the MOLE program the formation of pores with channel diameters of 1.2-1.6 and 1.4-4.6 nm in a model structure formed from two and four VirE2 molecules, respectively. Using...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Volokhina I, Gusev Y, Mazilov S, Chumakov M Tags: J Bioinform Comput Biol Source Type: research

Evaluating mixture models for building RNA knowledge-based potentials.
Abstract Ribonucleic acid (RNA) molecules play important roles in a variety of biological processes. To properly function, RNA molecules usually have to fold to specific structures, and therefore understanding RNA structure is vital in comprehending how RNA functions. One approach to understanding and predicting biomolecular structure is to use knowledge-based potentials built from experimentally determined structures. These types of potentials have been shown to be effective for predicting both protein and RNA structures, but their utility is limited by their significantly rugged nature. This ruggedness (and hence...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Sim AY, Schwander O, Levitt M, Bernauer J Tags: J Bioinform Comput Biol Source Type: research

Flexible and robust networks.
Abstract We consider networks with two types of nodes. The v-nodes, called centers, are hyperconnected and interact with one another via many u-nodes, called satellites. This centralized architecture, widespread in gene networks, possesses two fundamental properties. Namely, this organization creates feedback loops that are capable of generating practically any prescribed patterning dynamics, chaotic or periodic, or having a number of equilibrium states. Moreover, this organization is robust with respect to random perturbations of the system. PMID: 22809346 [PubMed - in process]
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Vakulenko SA, Radulescu O Tags: J Bioinform Comput Biol Source Type: research

Modeling of three dimensional structure of human alpha-fetoprotein complexed with diethylstilbestrol: docking and molecular dynamics simulation study.
Abstract It has been long experimentally demonstrated that human alpha-fetoprotein (HAFP) has an ability to bind immobilized estrogens with the most efficiency for synthetic estrogen analog - diethylstilbestrol (DES). However, the question remains why the human AFP (HAFP), unlike rodent AFP, cannot bind free estrogens. Moreover, despite the fact that AFP was first discovered more than 50 years ago and is presently recognized as a "golden standard" among onco-biomarkers, its three-dimensional (3D) structure has not been experimentally solved yet. In this work using MODELLER program, we generated 3D model of HAFP on ...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Terentiev AA, Moldogazieva NT, Levtsova OV, Maximenko DM, Borozdenko DA, Shaitan KV Tags: J Bioinform Comput Biol Source Type: research

Beyond comparing means: the usefulness of analyzing interindividual variation in gene expression for identifying genes associated with cancer development.
Abstract Identifying genes associated with cancer development is typically accomplished by comparing mean expression values in normal and tumor tissues, which identifies differentially expressed (DE) genes. Interindividual variation (IV) in gene expression is indirectly included in DE gene identification because given the same absolute differences in means, genes with lower variance tend to have lower p-values. We explored the direct use of IV in gene expression to identify candidate genes associated with cancer development. We focused on prostate (PCa) and lung (LC) cancers and compared IV in the expression level ...
Source: Journal of Bioinformatics and Computational Biology - April 1, 2012 Category: Bioinformatics Authors: Gorlov IP, Byun J, Zhao H, Logothetis CJ, Gorlova OY Tags: J Bioinform Comput Biol Source Type: research

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Comput Phys Commun. 2012 Apr;183(4):947-959 Authors: Seebacher J, Kendl A Abstract Linear kinetic Monte Carlo particle transport models are frequently employed in fusion plasma simulations to quantify atomic and surface effects on the main plasma flow dynamics. Separate codes are used for transport of neutral particles (incl. radiation) and charged particles (trace impurity ions). Integration of both modules into main plasma fluid solvers provides then self-consistent solutions, in principle. The required interfaces are far from trivial, because rapid atomic processes in particular in the edge region of fusion ...
Source: Computer Physics Communications - April 1, 2012 Category: Bioinformatics Authors: Seebacher J, Kendl A Tags: Comput Phys Commun Source Type: research

A new protein graph model for function prediction.
Abstract As several structural proteomic projects are producing an increasing number of protein structures with unknown function, methods that can reliably predict protein functions from protein structures are in urgent need. In this paper, we present a method to explore the clustering patterns of amino acids on the 3-dimensional space for protein function prediction. First, amino acid residues on a protein structure are clustered into spatial groups using hierarchical agglomerative clustering, based on the distance between them. Second, the protein structure is represented using a graph, where each node denotes a ...
Source: Computational Biology and Chemistry - April 1, 2012 Category: Bioinformatics Authors: Alvarez MA, Yan C Tags: Comput Biol Chem Source Type: research

Evolving kinetics of gene expression in stochastic environments.
Abstract Recent studies have shown that the in vivo dynamics of RNA numbers in bacteria is regulated, to a great extent, by the kinetics of rate limiting steps in transcription. Strong evidence suggests that the kinetics of these steps is sequence dependent. We investigate the selective advantages of rate limiting steps of differing kinetics. For that, we model the kinetics of expression of a gene responsible for promoting cell division at the expense of resources in the environment in individual cells of a population. We model mutations that affect the kinetics of the rate limiting steps and selective pressure in ...
Source: Computational Biology and Chemistry - April 1, 2012 Category: Bioinformatics Authors: Häkkinen A, Ribeiro AS Tags: Comput Biol Chem Source Type: research

GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection.
Abstract Finding genes associated with a disease is an important issue in the biomedical area and many gene prioritization methods have been proposed for this goal. Among these, network-based approaches are recently proposed and outperformed functional annotation-based ones. Here, we introduce a novel Cytoscape plug-in, GPEC, to help identify putative genes likely to be associated with specific diseases or pathways. In the plug-in, gene prioritization is performed through a random walk with restart algorithm, a state-of-the art network-based method, along with a gene/protein relationship network. The plug-in also a...
Source: Computational Biology and Chemistry - April 1, 2012 Category: Bioinformatics Authors: Le DH, Kwon YK Tags: Comput Biol Chem Source Type: research

A comparative proteomic study identified LRPPRC and MCM7 as putative actors in imatinib mesylate cross-resistance in Lucena cell line
Conclusions: Through the data presented in this work, we show the relevance of MDR to IM therapy. In addition, our proteomic approach identified candidate actors involved in resistance, which could lead to additional information on BCR-ABL-independent molecular mechanisms.
Source: Proteome Science - March 30, 2012 Category: Bioinformatics Authors: Stephany CorreaLuciana PizzattiBarbara Du RocherAndre MencalhaDaniela PintoEliana Abdelhay Source Type: research

A new algorithm for quantifying binding site pattern similarity with applications for Next Generation Sequencing.
Abstract New sources of regulatory data, such as transcription factor ChIP-seq experiments, can yield important insights into biological function through downstream analysis of motifs. Position Frequency Matrices (PFMs) are a standard format for representing transcription factor binding patterns. Comparison measures between these binding patterns are necessary to allow more sophisticated detection and classification of regulatory sequences. In this work we have developed a novel algorithm for gapped alignment of PFMs called PfmSim. We compare our measure with a standard measure, Sandelin and Wasserman, on similarit...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Bible PW, Loganantharaj R Tags: Int J Bioinform Res Appl Source Type: research

An effective graph-based clustering technique to identify coherent patterns from gene expression data.
Abstract This paper presents an effective parameter-less graph based clustering technique (GCEPD). GCEPD produces highly coherent clusters in terms of various cluster validity measures. The technique finds highly coherent patterns containing genes with high biological relevance. Experiments with real life datasets establish that the method produces clusters that are significantly better than other similar algorithms in terms of various quality measures. PMID: 22450268 [PubMed - in process]
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Priyadarshini G, Sarmah R, Chakraborty B, Bhattacharyya DK, Kalita JK Tags: Int J Bioinform Res Appl Source Type: research

Large margin classifiers and Random Forests for integrated biological prediction.
Abstract Incorporating various sources of biological information is important for biological discovery. For example, genes have a multiview representation. They can be represented by features such as sequence length and pairwise similarities. Hence, the types vary from numerical features to categorical features. We propose a large margin Random Forests (RF) classification approach based on RF proximity kernals. Random Forests accommodate mixed data types naturally. The performance on four biological datasets is promising compared with other state of the art methods including Support Vector Machines (SVMs) and RF cl...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Liu S, Chen Y, Wilkins D Tags: Int J Bioinform Res Appl Source Type: research

Combining gene expression and interaction network data to improve kidney lesion score prediction.
We present a method for predicting lesions using combination of statistical and biological feature selection methods along with an ensemble learning technique. Results show that combining highly interacting genes (Hub Genes) from protein-protein interaction network with genes selected by squared t-test method brings the most accurate kidney lesion score predictor. PMID: 22450270 [PubMed - in process]
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Moulavi D, Hajiloo M, Sander J, Halloran PF, Greiner R Tags: Int J Bioinform Res Appl Source Type: research

Detecting molecular selection on single amino acid replacements.
Abstract Amino acid property methods have repeatedly proven more sensitive than nucleotide-based methods, especially to the subtle influences of selection on Single Nucleotide Polymorphisms (SNPs). The purpose of this study is to evaluate the effects of population sampling and sliding window size on the sensitivity of one amino acid based method by assessing drug resistant SNPs from the HIV-1 gag-pol gene. The analysis of most of the SNPs produced positive results. There was not a trend in terms of properties affected most often, but sliding window size affected results more than population sampling. PMID: 2245...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: McClellan DA Tags: Int J Bioinform Res Appl Source Type: research

Computational analysis of adaptive antigenic mutations of the human influenza hemagglutinin for vaccine strain selection.
Abstract The adaptive evolution of the hemagglutinin (HA) segment of the human influenza H1N1 and H3N2 viruses is not well understood due to antigenic mutations under selection pressures. This paper identified significant antigenic selection sites and discussed the structural relevance of these mutations. We discovered four positively selected sites for H1N1 (position 206 for the 1A lineage - 2009 swine influenza, and positions 144, 190, and 192 for the 1B lineage), and eight positively selected sites for H3N2 with the loop regions near residues 157 and 225 as the latest antigenic mutations, which may be targeted f...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Rickert JD, Herpy TA, Zhong H, Lu G Tags: Int J Bioinform Res Appl Source Type: research

Evolution of bacterial ribosomal protein L1.
Abstract Search vectors composed of Gly, Ala, Arg, and Pro (GARP) residues retrieve 98% of each of the ribosomal proteins in prokaryotic species with no false hits. Different combinations of G, A, R and P and insertions differentiate each ribosomal protein from all others. Amino acids in two sequence positions separate Gram+ from Gram- bacteria. Specific residues separate proteins of cyanobacteria and chloroplasts from all other species. Structural information played an essential role in developing a GARP based technique to achieve perfect sequence alignment. It is possible to understand why GARP residues are 100% ...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Duax WL, Huether R, Dziak D Tags: Int J Bioinform Res Appl Source Type: research

Application of nanotechnology in cancer: a review.
Abstract Cancer nanotechnology is an interdisciplinary area with broad applications. The basic rationale is that nanometre-sized particles, when linked with tumour-targeting ligands, can be used to target tumour antigens. It is difficult to target the abnormal cells in cancer by the conventional method of the drug delivery. Nanotechnology is probably the only method that can be used for site-specific action without causing the side effects. Different cancer detection techniques like Carbon Nanotubes (CNTs), nanorods and biosensors are available. This review paper gives an idea about the possible potential of nanote...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Kolhe S, Parikh K Tags: Int J Bioinform Res Appl Source Type: research

New encoded single-indicator sequences based on physico-chemical parameters for efficient exon identification.
Abstract The first step in gene identification problem based on genomic signal processing is to convert character strings into numerical sequences. These numerical sequences are then analysed spectrally or using digital filtering techniques for the period-3 peaks, which are present in exons (coding areas) and absent in introns (non-coding areas). In this paper, we have shown that single-indicator sequences can be generated by encoding schemes based on physico-chemical properties. Two new methods are proposed for generating single-indicator sequences based on hydration energy and dipole moments. The proposed methods...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Meher JK, Meher PK, Dash GN, Raval MK Tags: Int J Bioinform Res Appl Source Type: research

Discovering best candidates for Hepatocellular Carcinoma (HCC) by in-silico techniques and tools.
Abstract Protein-ligand interaction plays an important role in structural-based drug designing. The aim of this work is to select new possible candidates for HCC by in-silico drug design using bioinformatics techniques and tool. Essential proteins were targeted for HCC metastasis; drugs were designed for them by using ligand-based drug design based on active model drugs. The study considered BCL-XL and FGF proteins and the commercially available drugs against HCC. The receptor was docked to those drugs and the energy values were obtained using the Molecular Operating Environment (MOE) docking software. According to...
Source: International Journal of Bioinformatics Research and Applications - March 29, 2012 Category: Bioinformatics Authors: Mabrouk MS Tags: Int J Bioinform Res Appl Source Type: research

Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: with application to major depressive disorder
Conclusions: The proposed framework simultaneously considers correction for confounding variables, selection of effective confounders, random effects from paired design and integration by meta-analysis. The approach improved disease-related biomarker and pathway detection, which greatly enhanced understanding of MDD neurobiology. The statistical framework can be applied to similar experimental design encountered in other complex and heterogeneous diseases.
Source: BMC Bioinformatics - Latest articles - March 29, 2012 Category: Bioinformatics Authors: Xingbin WangYan LinChi SongEtienne SibilleGeorge Tseng Source Type: research

Chado Controller: advanced annotation management with a community annotation system
Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. Availability: The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Guignon, V., Droc, G., Alaux, M., Baurens, F.-C., Garsmeur, O., Poiron, C., Carver, T., Rouard, M., Bocs, S. Tags: DATABASES AND ONTOLOGIES Source Type: research

pymzML--Python module for high-throughput bioinformatics on mass spectrometry data
Summary: pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra. Availability and implementation: pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed. Contact: christian@fufezan.net
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., Fufezan, C. Tags: DATA AND TEXT MINING Source Type: research

Mytoe: automatic analysis of mitochondrial dynamics
We present Mytoe, a tool for analyzing mitochondrial morphology and dynamics from fluorescence microscope images. The tool provides automated quantitative analysis of mitochondrial motion by optical flow estimation and of morphology by segmentation of individual branches of the network-like structure of the organelles. Mytoe quantifies several features of individual branches, such as length, tortuosity and speed, and of the macroscopic structure, such as mitochondrial area and degree of clustering. We validate the methods and apply them to the analysis of sequences of images of U2OS human cells with fluorescently labeled m...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Lihavainen, E., Makela, J., Spelbrink, J. N., Ribeiro, A. S. Tags: SYSTEMS BIOLOGY Source Type: research

IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data
Summary: The application of emerging metabolomics technologies to the comprehensive investigation of cellular biochemistry has been limited by bottlenecks in data processing, particularly noise filtering and metabolite identification. IDEOM provides a user-friendly data processing application that automates filtering and identification of metabolite peaks, paying particular attention to common sources of noise and false identifications generated by liquid chromatography–mass spectrometry (LC–MS) platforms. Building on advanced processing tools such as mzMatch and XCMS, it allows users to run a comprehensive pip...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Creek, D. J., Jankevics, A., Burgess, K. E. V., Breitling, R., Barrett, M. P. Tags: SYSTEMS BIOLOGY Source Type: research

Estimating population diversity with CatchAll
We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample ‘frequency count’ data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program. Availability: Free executable downloads for Linux, Windows and Mac OS...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Bunge, J., Woodard, L., Bohning, D., Foster, J. A., Connolly, S., Allen, H. K. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

xQTL workbench: a scalable web environment for multi-level QTL analysis
Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the ...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Arends, D., van der Velde, K. J., Prins, P., Broman, K. W., Moller, S., Jansen, R. C., Swertz, M. A. Tags: GENETICS AND POPULATION ANALYSIS Source Type: research

DOMIRE: a web server for identifying structural domains and their neighbors in proteins
Summary: The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query, a list of structural neighbors and their alignments are provided. DOMIRE, by displaying the protein structural domain organization, can...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Samson, F., Shrager, R., Tai, C.-H., Sam, V., Lee, B., Munson, P. J., Gibrat, J.-F., Garnier, J. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Improving your target-template alignment with MODalign
Summary: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all ...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Barbato, A., Benkert, P., Schwede, T., Tramontano, A., Kosinski, J. Tags: STRUCTURAL BIOINFORMATICS Source Type: research

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
Summary: Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Availability: Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further in...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Bonnal, R. J. P., Aerts, J., Githinji, G., Goto, N., MacLean, D., Miller, C. A., Mishima, H., Pagani, M., Ramirez-Gonzalez, R., Smant, G., Strozzi, F., Syme, R., Vos, R., Wennblom, T. J., Woodcroft, B. J., Katayama, T., Prins, P. Tags: SEQUENCE ANALYSIS Source Type: research

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
Summary: With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor, AMPHORA2 has several major enhancements and new functions: it has a greatly expanded phylogenetic marker database and can analyze both bacterial and archaeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogenetic accuracy; it ...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Wu, M., Scott, A. J. Tags: SEQUENCE ANALYSIS Source Type: research

Spliceman--a computational web server that predicts sequence variations in pre-mRNA splicing
Summary: It was previously demonstrated that splicing elements are positional dependent. We exploited this relationship between location and function by comparing positional distributions between all possible 4096 hexamers around a database of human splice sites. The distance measure used in this study found point mutations that produced higher distances disrupted splicing, whereas point mutations with smaller distances generally had no effect on splicing. Reasoning the idea that functional splicing elements have signature positional distributions around constitutively spliced exons, we introduce Spliceman—an online ...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Lim, K. H., Fairbrother, W. G. Tags: SEQUENCE ANALYSIS Source Type: research

WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms
We present an accurate and fast web server, WegoLoc for predicting subcellular localization of proteins based on sequence similarity and weighted Gene Ontology (GO) information. A term weighting method in the text categorization process is applied to GO terms for a support vector machine classifier. As a result, WegoLoc surpasses the state-of-the-art methods for previously used test datasets. WegoLoc supports three eukaryotic kingdoms (animals, fungi and plants) and provides human-specific analysis, and covers several sets of cellular locations. In addition, WegoLoc provides (i) multiple possible localizations of input pro...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Chi, S.-M., Nam, D. Tags: SEQUENCE ANALYSIS Source Type: research

SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments
Summary: Both alignment generation and visualization are important processes for producing biologically meaningful sequence alignments. Computational tools that combine reliable, automated and semi-automated approaches to produce secondary structure-based alignments with an appropriate visualization of the results are rare. We have developed SBAL, a tool to generate and edit secondary structure-based sequence alignments. It is easy to install and provides a user-friendly interface. Sequence alignments are displayed, with secondary structure assignments mapped to their corresponding regions in the sequence by using a simple...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Wang, C. K., Broder, U., Weeratunga, S. K., Gasser, R. B., Loukas, A., Hofmann, A. Tags: SEQUENCE ANALYSIS Source Type: research

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads
Summary: We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such breakpoints can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads. Availability: htt...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Sun, R., Love, M. I., Zemojtel, T., Emde, A.-K., Chung, H.-R., Vingron, M., Haas, S. A. Tags: GENOME ANALYSIS Source Type: research

ArchTEx: accurate extraction and visualization of next-generation sequence data
We present an algorithm, ArchTEx (Architectural Tag Extender), which identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension. Availability and implementation: ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/ Contact: mjbuck@buffalo.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Lai, W. K. M., Bard, J. E., Buck, M. J. Tags: GENOME ANALYSIS Source Type: research

vHOG, a multispecies vertebrate ontology of homologous organs groups
We describe the vertebrate Homologous Organs Groups ontology, vHOG, used to compare expression patterns between species. Results: vHOG is a multispecies anatomical ontology for the vertebrate lineage. It is based on the HOGs used in the Bgee database of gene expression evolution. vHOG version 1.4 includes 1184 terms, follows OBO principles and is based on the Common Anatomy Reference Ontology (CARO). vHOG only describes structures with historical homology relations between model vertebrate species. The mapping to species-specific anatomical ontologies is provided as a separate file, so that no homology hypothesis is stated...
Source: Bioinformatics - March 29, 2012 Category: Bioinformatics Authors: Niknejad, A., Comte, A., Parmentier, G., Roux, J., Bastian, F. B., Robinson-Rechavi, M. Tags: DATABASES AND ONTOLOGIES Source Type: research