PROBEmer: A web-based software tool for selecting optimal DNA oligos

PROBEmer (http://probemer.cs.loyola.edu) is a web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. The software has been used to obtain genus-specific prokaryotic probes based on the 16S rRNA gene, gene-specific probes for expression analyses and PCR primers. In this paper, we describe how to use PROBEmer, the computational methods it employs, and experimental results for oligos identified by this software tool.     

solGS: a web-based tool for genomic selection

Background

Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide markers and statistical complexity, however, is a serious challenge in data management, analysis, and sharing. A bioinformatics infrastructure for data storage and access, and user-friendly web-based tool for analysis and sharing output is needed to make GS more practical for breeders.

Results

We have developed a web-based tool, called solGS, for predicting genomic estimated breeding values (GEBVs) of individuals, using a Ridge-Regression Best Linear Unbiased Predictor (RR-BLUP) model. It has an intuitive web-interface for selecting a training population for modeling and estimating genomic estimated breeding values of selection candidates. It estimates phenotypic correlation and heritability of traits and selection indices of individuals. Raw data is stored in a generic database schema, Chado Natural Diversity, co-developed by multiple database groups. Analysis output is graphically visualized and can be interactively explored online or downloaded in text format. An instance of its implementation can be accessed at the NEXTGEN Cassava breeding database, http://cassavabase.org/solgs.

Conclusions

solGS enables breeders to store raw data and estimate GEBVs of individuals online, in an intuitive and interactive workflow. It can be adapted to any breeding program.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0398-7) contains supplementary material, which is available to authorized users.     

RotaC: A web-based tool for the complete genome classification of group A rotaviruses

Background  

Group A rotaviruses are the most common cause of severe diarrhea in infants and children worldwide and continue to have a major global impact on childhood morbidity and mortality. In recent years, considerable research efforts have been devoted to the development of two new live, orally administered vaccines. Although both vaccines have proven to confer a good protection against severe rotavirus gastroenteritis, these vaccines will have to be screened and may have to be updated regularly to reflect temporal and spatial genotype fluctuations. In this matter, the genetic characterization of circulating and new emerging rotavirus strains will need to be compulsory and accurate. An extended classification system for rotaviruses in which all the 11 genomic RNA segments are used, has been proposed recently. The use of this classification system will help to elucidate the role of gene reassortments in the generation of genetic diversity, host range restriction, co-segregation of certain gene segments, and in adaptation to a new host species.     

3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison

Background

As Next-Generation Sequencing data becomes available, existing hardware environments do not provide sufficient storage space and computational power to store and process the data due to their enormous size. This is and will be a frequent problem that is encountered everyday by researchers who are working on genetic data. There are some options available for compressing and storing such data, such as general-purpose compression software, PBAT/PLINK binary format, etc. However, these currently available methods either do not offer sufficient compression rates, or require a great amount of CPU time for decompression and loading every time the data is accessed.

Results

Here, we propose a novel and simple algorithm for storing such sequencing data. We show that, the compression factor of the algorithm ranges from 16 to several hundreds, which potentially allows SNP data of hundreds of Gigabytes to be stored in hundreds of Megabytes. We provide a C++ implementation of the algorithm, which supports direct loading and parallel loading of the compressed format without requiring extra time for decompression. By applying the algorithm to simulated and real datasets, we show that the algorithm gives greater compression rate than the commonly used compression methods, and the data-loading process takes less time. Also, The C++ library provides direct-data-retrieving functions, which allows the compressed information to be easily accessed by other C++ programs.

Conclusions

The SpeedGene algorithm enables the storage and the analysis of next generation sequencing data in current hardware environment, making system upgrades unnecessary.     

BarleyExpress: a web-based submission tool for enriched microarray database annotations

BarleyExpress is a web-based microarray experiment data submission tool for BarleyBase, a public data resource of Affymetrix GeneChip data for plants. BarleyExpress uses the Plant Ontology vocabularies and enhances the MIAME guidelines to standardize the annotation of microarray gene expression experiments. In addition, BarleyExpress provides explicit support for factorial experiment design and template loading methods to ease the submission process for large experiments. AVAILABILITY: http://barleybase.org SUPPLEMENTARY INFORMATION: BarleyExpress Users Manual.     

RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes

Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they are annotated open reading frames or not. The tool successfully confirmed all reported TA systems, and spotted new putative loci upon screening of sequenced genomes. RASTA-Bacteria is publicly available at .     

NetAlign: a web-based tool for comparison of protein interaction networks

NetAlign is a web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs), which may derive from a common ancestor and disclose conserved topological organization of interactions in evolution. To exemplify the application of NetAlign, we perform two genome-scale comparisons with (1) the Escherichia coli PIN against the Helicobacter pylori PIN and (2) the Saccharomyces cerevisiae PIN against the Caenorrhabditis elegans PIN. Many of the identified CoNSs correspond to known complexes; therefore, cross-species PIN comparison provides a way for discovery of conserved modules. In addition, based on the species-to-species differences in CoNSs, we reformulate the problems of protein-protein interaction (PPI) prediction and species divergence from a network perspective. AVAILABILITY: http://www1.ustc.edu.cn/lab/pcrystal/NetAlign.     

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees

SUMMARY: We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length. AVAILABILITY: The software is implemented as a Java applet at http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html. It is also available on request from the authors.     

A web-based tool for principal component and significance analysis of microarray data

We have developed a program for microarray data analysis, which features the false discovery rate for testing statistical significance and the principal component analysis using the singular value decomposition method for detecting the global trends of gene-expression patterns. Additional features include analysis of variance with multiple methods for error variance adjustment, correction of cross-channel correlation for two-color microarrays, identification of genes specific to each cluster of tissue samples, biplot of tissues and corresponding tissue-specific genes, clustering of genes that are correlated with each principal component (PC), three-dimensional graphics based on virtual reality modeling language and sharing of PC between different experiments. The software also supports parameter adjustment, gene search and graphical output of results. The software is implemented as a web tool and thus the speed of analysis does not depend on the power of a client computer. AVAILABILITY: The tool can be used on-line or downloaded at http://lgsun.grc.nia.nih.gov/ANOVA/     

Primer Design Assistant (PDA): A web-based primer design tool

Primer Design Assistant (PDA) is a web interface primer design service combined with thermodynamic theory to evaluate the fitness of primers. It runs in a Linux-Apache-MySQL-PHP structure on a PC equipped with dual CPU (Intel Pentium III 1.4 GHz) and 512 Mb of RAM. A succinct user interface of PDA is accomplished by built-in parameters setting. Advanced options on 5' GC content, 3' GC content, dimer check and hairpin check are available. The option of covered region constrains the PCR product to cover a user-defined segment. PDA accepts single sequence query or multiple ones in FASTA format. It produces optimal and homogenous primer pairs that meet the need in experimental design with large-scaled PCR amplifications. Considering the system loading, the size of a submitted sequence is limited to 10 kb and the total sequence number in a query is limited to 20. The authors may be contacted regarding other requirements for primer design. The web application can be found at http://dbb.nhri.org.tw/primer/.     

SENSE tool: easy-to-use web-based tool to calculate food product environmental impact

Purpose

The purpose of the European SENSE project was to define an integral system to assess and communicate the environmental impacts of food products and to develop a web-based tool for Small and Medium size Enterprises (SMEs). The tool has been tested in salmon, beef-and-dairy, and fruit juice production sectors.

Methods

The SENSE project has evaluated several existing methodologies for environmental impact assessment over the life cycle including also social aspects, in order to deliver a new integral system for the environmental and social assessment of agricultural and aquaculture food products.

Results and discussion

The system includes a standardization of a data gathering system, a selection of relevant key environmental performance indicators for food supply chains and a common methodology to perform simplified life cycle impact assessment. The results are based on collected information on the use of resources and emissions generated along the supply chain of food or drink products. The main result is a web-based software tool that is based on a summation of the partial impacts of the different steps in food supply chains. In this software, different actors in the supply chain can enter their own data and link them to the data of other companies. The results obtained in the tool could be used for at least six different approaches: (i) environmental impact assessment of the product, (ii) food chain hot spot identification, (iii) comparison of hypothetical or real improvement scenarios, (iv) assessment of the environmental impact development over the years, (v) benchmarking opportunity for the companies, and (vi) a business to business communication strategy. The scientific robustness of the tool has been tested comparing the obtained results with the same analysis with commercial software.

Conclusions

The SENSE tool is a simplified tool designed for food and drink SMEs to assess their sustainability on their own. This cannot be fully compared to a complete LCA study. The testing with SMEs showed that they need additional support for filling in the questionnaires correctly and interpret the results. The simplified evaluation of environmental impacts based on a life cycle approach could lead to benefits to SMEs within the food industry. The future application and development of the tool will be focused on adapting the tool to the Product Environmental Footprint initiative requirements and self-assessment opportunities.

     

MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences

The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming.     

SMART: a web-based tool for the study of genetically mobile domains

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de ). More than 400 domain families found in signalling, extra-cellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.     

ProFAT: a web-based tool for the functional annotation of protein sequences

Background  

The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches.     

PGMapper: a web-based tool linking phenotype to genes

SUMMARY: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species. AVAILABILITY: Available online at http://www.genediscovery.org/pgmapper/index.jsp.     

A universal approach for promoter strength evaluation supported by the web-based tool PromCal

In genetic engineering, gene expression is often modulated by replacements in promoter regions. Any deliberate intervention into the regulatory elements requires a subsequent evaluation based on analysis of reporter proteins. We have developed a new and rapid approach for characterization of promoter activity in which promoter strengths are determined by antibiotic resistance level. Values are expressed in comparison with those obtained from the reference promoter using the kanamycin resistance (aminoglycoside 3′-phosphotransferase) gene as a reporter. The new assay vector pSB1K0prom enables straightforward cloning of promoters or their subparts; therefore, mutations in different elements of the promoter region are easily introduced and analyzed. A series of promoters can be examined in parallel because no protein analysis is required other than determination of bacterial growth rates in the presence of increasing kanamycin concentrations. An internet application called PromCal for evaluation of experimental data has also been developed and is freely accessible at http://web.fkkt.uni-lj.si/biokemija/nskrlj/tools/PromCal.php.