AutoAssemblyD: a graphical user interface system for several genome assemblers

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates.

Availability

AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.     

Meeting highlights: genome informatics

We bring you the highlights of the second Joint Cold Spring Harbor Laboratory and Wellcome Trust 'Genome Informatics' Conference, organized by Ewan Birney, Suzanna Lewis and Lincoln Stein. There were sessions on in silico data discovery, comparative genomics, annotation pipelines, functional genomics and integrative biology. The conference included a keynote address by Sydney Brenner, who was awarded the 2002 Nobel Prize in Physiology or Medicine (jointly with John Sulston and H. Robert Horvitz) a month later.     

The missing graphical user interface for genomics

The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface.     

GenomeMatcher: A graphical user interface for DNA sequence comparison

Background  

The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed.     

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing

Background

Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics.

Results

We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved.

Conclusion

The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.     

The case for cloud computing in genome informatics

With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.     

limmaGUI: a graphical user interface for linear modeling of microarray data

SUMMARY: limmaGUI is a graphical user interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of differential expression in complex experiments. limmaGUI provides an interface to the statistical methods of the limma package for R, and is itself implemented as an R package. The software provides point and click access to a range of methods for background correction, graphical display, normalization, and analysis of microarray data. Arbitrarily complex microarray experiments involving multiple RNA sources can be accomodated using linear models and contrasts. Empirical Bayes shrinkage of the gene-wise residual variances is provided to ensure stable results even when the number of arrays is small. Integrated support is provided for quantitative spot quality weights, control spots, within-array replicate spots and multiple testing. limmaGUI is available for most platforms on the which R runs including Windows, Mac and most flavors of Unix. AVAILABILITY: http://bioinf.wehi.edu.au/limmaGUI.     

A-Cell: graphical user interface for the construction of biochemical reaction models

SUMMARY: A-Cell is a tool for constructing models of complex and complicated biochemical reactions. An important feature of A-Cell is its graphical user interface for constructing biochemical reactions. In addition, it has a capability of importing previously constructed models, combining them, and constructing a comprehensive model. The simulation program for the model is automatically generated by A-cell.     

SimHap GUI: An intuitive graphical user interface for genetic association analysis

Background

The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways.

Results

annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools.

Conclusion

annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.     

GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness

In view of the recent explosion in genome sequence data, and the 200 or more complete genome sequences currently available, the importance of genome-scale bioinformatics analysis is increasing rapidly. However, computational genome informatics analyses often lack a statistical assessment of their sensitivity to the completeness of the functional annotation. Therefore, a pre-analysis method to automatically validate the sensitivity of computational genome analyses with regard to genome annotation completeness is useful for this purpose. In this report we developed the Gene Prediction Accuracy Classification (GPAC) test, which provides statistical evidence of sensitivity by repeating the same analysis for five different gene groups (classified according to annotation accuracy level), and for randomly sampled gene groups, with the same number of genes as each of the five classified groups. Variability in these results is then assessed, and if the results vary significantly with different data subsets, the analysis is considered "sensitive" to annotation completeness, and careful selection of data is advised prior to the actual in silico analysis. The GPAC test has been applied to the analyses of Sakai et al., 2001, and Ohno et al., 2001, and it revealed that the analysis of Ohno et al. was more sensitive to annotation completeness. It showed that GPAC could be employed to ascertain the sensitivity of an analysis. The GPAC bendhmarking software is freely available in the latest G-language Genome Analysis Environment package, at http://www.g-language.org/.     

affylmGUI: a graphical user interface for linear modeling of single channel microarray data

SUMMARY: affylmGUI is a graphical user interface (GUI) to an integrated workflow for Affymetrix microarray data. The user is able to proceed from raw data (CEL files) to QC and pre-processing, and eventually to analysis of differential expression using linear models with empirical Bayes smoothing. Output of the analysis (tables and figures) can be exported to an HTML report. The GUI provides user-friendly access to state-of-the-art methods embodied in the Bioconductor software repository. AVAILABILITY: affylmGUI is an R package freely available from http://www.bioconductor.org. It requires R version 1.9.0 or later and tcl/tk 8.3 or later and has been successfully tested on Windows 2000, Windows XP, Linux (RedHat and Fedora distributions) and Mac OS/X with X11. Further documentation is available at http://bioinf.wehi.edu.au/affylmGUI CONTACT: keith@wehi.edu.au.     

The design of Jemboss: a graphical user interface to EMBOSS

DESIGN: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/     

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.     

A graphical user interface for BIOEQS: a program for simulating and analyzing complex biomolecular interactions

BIOEQS is a global analysis and simulation program for complex biomolecular interaction data developed during the 1990s. Its continued usefulness derives from the fact that it is based on a numerical solver for complex coupled biological equilibria rather than on closed-form analytical equations for the binding isotherms. Therefore, it is quite versatile, allowing easy testing of multiple binding models and analysis of systems too complex for closed-form solutions. However, a major drawback to a generalized use of this program has been the lack of a graphical user interface (GUI) for setting up the binding models and experimental conditions as well as for visualizing the results. We present here a new GUI for BIOEQS that should be useful in both research and teaching applications.     

GeneView: multi-language human gene mapping library with a graphical user interface

GeneView is a newly developed human gene mapping library systemthat works on an X-Window platform. This system is designedfor researchers who routinely utilize gene mapping data in thelaboratory but are unfamiliar with computer technology. GeneViewoffers various features, including friendly user interface,fast operation and visualization facility. Genetic loci aredisplayed graphically with an idiogram. This system can be operatedin multiple languages. A current version supports Japanese andEnglish, and can be easily expanded to include other languages.A prototype of GeneView is now installed on a SPARC (Sun4) workstation.Because of the X-Window platform, GeneView should be compatiblewith various types of workstations.