Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

Background  

DNA sequencing is used ubiquitously: from deciphering genomes[1] to determining the primary sequence of small RNAs (smRNAs) [2–5]. The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for ~700 smRNA sequences[6]. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study.     

RDMAS: a web server for RNA deleterious mutation analysis

Background  

The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness.     

PHOENIX, a web interface for (re)analysis of microarray data

Microarrays are tools to study the expression profile of an entire genome. Technology, statistical tools and biological knowledge in general have evolved over the past ten years and it is now possible to improve analysis of previous datasets. We have developed a web interface called PHOENIX that automates the analysis of microarray data from preprocessing to the evaluation of significance through manual or automated parameterization. At each analytical step, several methods are possible for (re)analysis of data. PHOENIX evaluates a consensus score from several methods and thus determines the performance level of the best methods (even if the best performing method is not known). With an estimate of the true gene list, PHOENIX can evaluate the performance of methods or compare the results with other experiments. Each method used for differential expression analysis and performance evaluation has been implemented in the PEGASE back-end package, along with additional tools to further improve PHOENIX. Future developments will involve the addition of steps (CDF selection, geneset analysis, meta-analysis), methods (PLIER, ANOVA, Limma), benchmarks (spike-in and simulated datasets), and illustration of the results (automatically generated report).     

COGNAT: a web server for comparative analysis of genomic neighborhoods

Background

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families.

Aim

We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server.

Results

Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002).

Reviewers

This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

     

WAMI: a web server for the analysis of minisatellite maps

Background  

Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time.     

GTC: A web server for integrating systems biology data with web tools and desktop applications

Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using many popular web-based and desktop applications.     

VARAN: a web server for variability analysis of DNA microarray experiments

SUMMARY: Here, we describe a tool for VARiability Analysis of DNA microarrays experiments (VARAN), a freely available Web server that performs a signal intensity based analysis of the log2 expression ratio variability deduced from DNA microarray data (one or two channels). Two modules are proposed: VARAN generator to compute a sliding windows analysis of the experimental variability (mean and SD) and VARAN analyzer to compare experimental data with an asymptotic variability model previously built with the generator module from control experiments. Both modules provide normalized intensity signals with five possible methods, log ratio values and a list of genes showing significant variations between conditions. AVAILABILITY: http://www.bionet.espci.fr/varan/ SUPPLEMENTARY INFORMATION: http://www.bionet.espci.fr/varan/help.html     

Zebra: a web server for bioinformatic analysis of diverse protein families

During evolution of proteins from a common ancestor, one functional property can be preserved while others can vary leading to functional diversity. A systematic study of the corresponding adaptive mutations provides a key to one of the most challenging problems of modern structural biology – understanding the impact of amino acid substitutions on protein function. The subfamily-specific positions (SSPs) are conserved within functional subfamilies but are different between them and, therefore, seem to be responsible for functional diversity in protein superfamilies. Consequently, a corresponding method to perform the bioinformatic analysis of sequence and structural data has to be implemented in the common laboratory practice to study the structure–function relationship in proteins and develop novel protein engineering strategies. This paper describes Zebra web server – a powerful remote platform that implements a novel bioinformatic analysis algorithm to study diverse protein families. It is the first application that provides specificity determinants at different levels of functional classification, therefore addressing complex functional diversity of large superfamilies. Statistical analysis is implemented to automatically select a set of highly significant SSPs to be used as hotspots for directed evolution or rational design experiments and analyzed studying the structure–function relationship. Zebra results are provided in two ways – (1) as a single all-in-one parsable text file and (2) as PyMol sessions with structural representation of SSPs. Zebra web server is available at http://biokinet.belozersky.msu.ru/zebra.     

IWS: integrated web server for protein sequence and structure analysis

Rapid increase in protein sequence information from genome sequencing projects demand the intervention of bioinformatics tools to recognize interesting gene-products and associated function. Often, multiple algorithms need to be employed to improve accuracy in predictions and several structure prediction algorithms are on the public domain. Here, we report the availability of an Integrated Web-server as a bioinformatics online package dedicated for in-silico analysis of protein sequence and structure data (IWS). IWS provides web interface to both in-house and widely accepted programs from major bioinformatics groups, organized as 10 different modules. IWS also provides interactive images for Analysis Work Flow, which will provide transparency to the user to carry out analysis by moving across modules seamlessly and to perform their predictions in a rapid manner. AVAILABILITY: IWS IS AVAILABLE FROM THE URL: http://caps.ncbs.res.in/iws.     

WebAllergen: a web server for predicting allergenic proteins

WebAllergen is a web server that predicts the potential allergenicity of proteins. The query protein will be compared against a set of prebuilt allergenic motifs that have been obtained from 664 known allergen proteins. The query will also be compared with known allergens that do not have detectable allergenic motifs. Moreover, users are allowed to upload their own allergens as alternative training sequences on which a new set of allergenic motifs will be built. The query sequences can also be compared with these motifs. AVAILABILITY: http://weballergen.bii.a-star.edu.sg/     

COGcollator: a web server for analysis of distant relationships between homologous protein families

Background

The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.

Aim

We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server.

Results

Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1.

Reviewers

This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.

     

MRSD: a web server for metabolic route search and design

SUMMARY: We present a tool called MRSD (Metabolic Route Search and Design) to search and design routes based on the weighted compound transform diagraph. The search submodule returns routes between a source and product compound within seconds in the network of one or multiple organisms based on data from KEGG. The design submodule designs a route from an appointed compound in an interactive mode. The two complementary functions, Metabolic Route Search and Design, can be broadly used in biosynthesis, bio-pharmaceuticals and the other related fields. AVAILABILITY: bioinfo.ustc.edu.cn/softwares/MRSD/.     

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

hmChIP is a database of genome-wide chromatin immunoprecipitation (ChIP) data in human and mouse. Currently, the database contains 2016 samples from 492 ChIP-seq and ChIP-chip experiments, representing a total of 170 proteins and 11 069 914 protein-DNA interactions. A web server provides interface for database query. Protein-DNA binding intensities can be retrieved from individual samples for user-provided genomic regions. The retrieved intensities can be used to cluster samples and genomic regions to facilitate exploration of combinatorial patterns, cell-type dependencies, and cross-sample variability of protein-DNA interactions. AVAILABILITY: http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl.     

RANKPROP: a web server for protein remote homology detection

Summary: We present a large-scale implementation of the RANKPROPprotein homology ranking algorithm in the form of an openlyaccessible web server. We use the NRDB40 PSI-BLAST all-versus-allprotein similarity network of 1.1 million proteins to constructthe graph for the RANKPROP algorithm, whereas previously, resultswere only reported for a database of 108 000 proteins. We alsodescribe two algorithmic improvements to the original algorithm,including propagation from multiple homologs of the query andbetter normalization of ranking scores, that lead to higheraccuracy and to scores with a probabilistic interpretation. Availability: The RANKPROP web server and source code are availableat http://rankprop.gs.washington.edu Contact: iain{at}nec-labs.com; noble{at}gs.washington.edu Associate Editor: Burkhard Rost     

XtalPred: a web server for prediction of protein crystallizability

XtalPred is a web server for prediction of protein crystallizability. The prediction is made by comparing several features of the protein with distributions of these features in TargetDB and combining the results into an overall probability of crystallization. XtalPred provides: (1) a detailed comparison of the protein's features to the corresponding distribution from TargetDB; (2) a summary of protein features and predictions that indicate problems that are likely to be encountered during protein crystallization; (3) prediction of ligands; and (4) (optional) lists of close homologs from complete microbial genomes that are more likely to crystallize. AVAILABILITY: The XtalPred web server is freely available for academic users on http://ffas.burnham.org/XtalPred