BLAST++: BLASTing queries in batches

BLAST++ is a tool that is integrated with NCBI BLAST, allowing multiple, say K, queries to be searched against a database concurrently. The results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but BLAST++ completes the processing in a much shorter time. AVAILABILITY: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Supplementary information: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++     

Identifying time-lagged gene clusters using gene expression data

MOTIVATION: Analysis of gene expression data can provide insights into the time-lagged co-regulation of genes/gene clusters. However, existing methods such as the Event Method and the Edge Detection Method are inefficient as they compare only two genes at a time. More importantly, they neglect some important information due to their scoring criterian. In this paper, we propose an efficient algorithm to identify time-lagged co-regulated gene clusters. The algorithm facilitates localized comparison and processes several genes simultaneously to generate detailed and complete time-lagged information for genes/gene clusters. RESULTS: We experimented with the time-series Yeast gene dataset and compared our algorithm with the Event Method. Our results show that our algorithm is not only efficient, but also delivers more reliable and detailed information on time-lagged co-regulation between genes/gene clusters. AVAILABILITY: The software is available upon request. CONTACT: jiliping@comp.nus.edu.sg SUPPLEMENTARY INFORMATION: Supplementary tables and figures for this paper can be found at http://www.comp.nus.edu.sg/~jiliping/p2.htm.     

SEGE: A database on 'intron less/single exonic' genes from eukaryotes

SUMMARY: Eukaryotes have both 'intron containing' and 'intron less' genes. Several databases are available for 'intron containing' genes in eukaryotes. In this note, we describe a database for 'intron less' genes from eukaryotes. 'Intron less' eukaryotic genes having prokaryotic architecture will help to understand gene evolution in a much simpler way unlike 'intron containing' genes. AVAILABILITY: SEGE is available at http://intron.bic.nus.edu.sg/seg/ CONTACT: mmeena@ntu.edu.sg     

LabArray: real-time imaging and analytical tool for microarrays

SUMMARY: Microarrays have been used to perform high-throughput genetic analyses such as single-nucleotide polymorphisms detection and microbial genome analysis. Some of these analyses require real-time monitoring of the hybridization signals with respect to a varying experimental condition, such as temperature. However, current microarray imaging and analysis packages typically do not possess such real-time capabilities. Therefore, microarray image analyses are often time-consuming and labour-intensive. LabArray was developed to expedite such processes by enabling real-time monitoring of microarray signals. AVAILABILITY: LabArray is available at http://www.eng.nus.edu.sg/civil/Labarray/labarray.htm CONTACT: cveliuwt@nus.edu.sg SUPPLEMENTARY INFORMATION: Screenshots and instructions for use are available at the above website.     

ExInt: an Exon Intron Database

The Exon/Intron Database (ExInt) stores information of all GenBank eukaryotic entries containing an annotated intron sequence. Data are available through a retrieval system, as flat-files and as a MySQL dump file. In this report we discuss several implementations added to ExInt, which is accessible at http://intron.bic.nus.edu.sg/exint/newexint/exint.html.     

Soap-HT-BLAST: high throughput BLAST based on Web services

SUMMARY: A high throughput Basic Local Alignment Search Tool (BLAST) system based on Web services is implemented. It provides an alternative BLAST service and allows users to perform multiple BLAST queries at one run in a distributed, parallel environment through the Internet. AVAILABILITY: It is available at http://mammoth.bii.a-star.edu.sg/webservices/htblast/index.html and at http://www.bii.a-star.edu.sg/jiren/download.html     

XdomView: protein domain and exon position visualization

SUMMARY: The relationship between intron distribution in the eukaryotic gene and protein structural elements is essential for understanding the origin and evolution of genes. XdomView is a web-based viewer mapping protein structural domains and intron positions in eukaryotic homologues to its tertiary structure. The association of sequence signals to 3D structure in XdomView provides a valuable visualization environment for eukaryotic gene organization, gene evolution, protein folding and protein structure classification. AVAILABILITY: Freely available from http://surya.bic.nus.edu.sg/xdom.     

datPAV--an online processing, analysis and visualization tool for exploratory investigation of experimental data

SUMMARY: Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalist to quickly assess the general characteristics of the data. This platform-independent software is designed as a generic tool to process and visualize data matrices. This tool explores organization of the data, detect errors and support basic statistical analyses. Processed data can be reused whereby different step-by-step data processing/analysis workflows can be created to carry out detailed investigation. The visualization option provides publication-ready graphics. Applications of this tool are demonstrated at the web site for three cases of metabolomics, environmental and hydrodynamic data analysis. AVAILABILITY: datPAV is available free for academic use at http://www.sdwa.nus.edu.sg/datPAV/.     

SUSPECTS: enabling fast and effective prioritization of positional candidates

SUMMARY: SUSPECTS is a web-based server which combines annotation and sequence-based approaches to prioritize disease candidate genes in large regions of interest. It uses multiple lines of evidence to rank genes quickly and effectively while limiting the effect of annotation bias to significantly improve performance. AVAILABILITY: SUSPECTS is freely available at http://www.genetics.med.ed.ac.uk/suspects/ SUPPLEMENTARY INFORMATION: A quick-start guide in Macromedia Flash format is available at http://www.genetics.med.ed.ac.uk/suspects/help.shtml and Excel spreadsheets detailing the comparative performance of the software are included as Supplementary material.     

TRMP: a database of therapeutically relevant multiple pathways

SUMMARY: Disease processes often involve crosstalks between proteins in different pathways. Different proteins have been used as separate therapeutic targets for the same disease. Synergetic targeting of multiple targets has been explored in combination therapy of a number of diseases. Potential harmful interactions of multiple targeting have also been closely studied. To facilitate mechanistic study of drug actions and a more comprehensive understanding the relationship between different targets of the same disease, it is useful to develop a database of known therapeutically relevant multiple pathways (TRMPs). Information about non-target proteins and natural small molecules involved in these pathways also provides useful hint for searching new therapeutic targets and facilitate the understanding of how therapeutic targets interact with other molecules in performing specific tasks. The TRMPs database is designed to provide information about such multiple pathways along with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, structural and functional information about each protein in the pathways. Cross links to other databases are also introduced to facilitate the access of information about individual pathways and proteins. AVAILABILITY: This database can be accessed at http://bidd.nus.edu.sg/group/trmp/trmp.asp and it currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions together with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. SUPPLEMENTARY INFORMATION: http://bidd.nus.edu.sg/group/trmp/sm.pdf     

MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules

SUMMARY: Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the first step in T-cell mediated immune response. To understand the structural principles governing MHC-specific peptide recognition and binding, we have developed the MHC-Peptide Interaction Database (MPID), containing sequence-structure-function information. MPID (version 1.2) contains curated x-ray crystallographic data on 86 MHC peptide complexes, with precomputed interaction parameters (solvent accessibility, hydrogen bonds, gap volume and gap index). A user-friendly web interface and query tools will facilitate the development of predictive algorithms for MHC-peptide binding from a structural viewpoint. AVAILABILITY: Freely accessible from http://surya.bic.nus.edu.sg/mpid.     

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

High-throughput sequencing is increasingly being used in combination with bisulfite (BS) assays to study DNA methylation at nucleotide resolution. Although several programmes provide genome-wide alignment of BS-treated reads, the resulting information is not readily interpretable and often requires further bioinformatic steps for meaningful analysis. Current post-alignment BS-sequencing programmes are generally focused on the gene-specific level, a restrictive feature when analysis in the non-coding regions, such as enhancers and intergenic microRNAs, is required. Here, we present Genome Bisulfite Sequencing Analyser (GBSA—http://ctrad-csi.nus.edu.sg/gbsa), a free open-source software capable of analysing whole-genome bisulfite sequencing data with either a gene-centric or gene-independent focus. Through analysis of the largest published data sets to date, we demonstrate GBSA’s features in providing sequencing quality assessment, methylation scoring, functional data management and visualization of genomic methylation at nucleotide resolution. Additionally, we show that GBSA’s output can be easily integrated with other high-throughput sequencing data, such as RNA-Seq or ChIP-seq, to elucidate the role of methylated intergenic regions in gene regulation. In essence, GBSA allows an investigator to explore not only known loci but also all the genomic regions, for which methylation studies could lead to the discovery of new regulatory mechanisms.     

Automatic 3D protein structure classification without structural alignment.

In this paper, we present a new scheme named ProtClass for automatic classification of three-dimensional (3D) protein structures. It is a dedicated and unified multiclass classification scheme. Neither detailed structural alignment nor multiple binary classifications are required in this scheme. We adopt a nearest neighbor-based classification strategy. We use a filter-and-refine scheme. In the first step, we filter out the improbable answers using the precalculated parameters from the training data. In the second, we perform a relatively more detailed nearest neighbor search on the remaining answers. We use very concise and effective encoding schemes of the 3D protein structures in both steps. We compare our proposed method against two other dedicated protein structure classification schemes, namely SGM and CPMine. The experimental results show that ProtClass is slightly better in accuracy than SGM and much faster. In comparison with CPMine, ProtClass is much more accurate, while their running times are about the same. We also compare ProtClass against a structural alignment-based classification scheme named DALI, which is found to be more accurate, but extremely slow. The software is available upon request from the authors. The supplementary information on ProtClass method can be found at: http://xena1.ddns.comp.nus.edu.sg/ approximately genesis/PClass.htm.     

MatAlign: precise protein structure comparison by matrix alignment

We propose a detailed protein structure alignment method named "MatAlign". It is a two-step algorithm. Firstly, we represent 3D protein structures as 2D distance matrices, and align these matrices by means of dynamic programming in order to find the initially aligned residue pairs. Secondly, we refine the initial alignment iteratively into the optimal one according to an objective scoring function. We compare our method against DALI and CE, which are among the most accurate and the most widely used of the existing structural comparison tools. On the benchmark set of 68 protein structure pairs by Fischer et al., MatAlign provides better alignment results, according to four different criteria, than both DALI and CE in a majority of cases. MatAlign also performs as well in structural database search as DALI does, and much better than CE does. MatAlign is about two to three times faster than DALI, and has about the same speed as CE. The software and the supplementary information for this paper are available at http://xena1.ddns.comp.nus.edu.sg/~genesis/MatAlign/.     

G-PRIMER: greedy algorithm for selecting minimal primer set

G-PRIMER, a web-based primer design program, has been developed to compute a minimal primer set specifically annealed to all the open reading frames in a given microbial genome. This program has been successfully used in the microarray experiment for analyzing the expression of genes in the Xanthomonas campestris genome. AVAILABILITY: It is available at http://mammoth.bii.a-star.edu.sg/gprimer/. Its source code is available upon request.     

Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies

A modification to Phred and program to detect heterogeneous positions, which is particularly useful in the identification of mutations and other abnormalities in Phred/Phrap genome assemblies. AVAILABILITY: The package is made available at http://glscompute.gis.a-star.edu.sg/~charlie/DHetero.html