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PubMed2005

GARSA: genomic analysis resources for sequence annotation.

SUMMARY: Growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools and genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analyzed using the system since it accepts (1) chromatograms, (2) download of sequences from GenBank, (3) Fasta files stored locally or (4) a combination of all three. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), Trypanosoma rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST). AVAILABILITY: The GARSA system is freely available under GPL license (http://www.biowebdb.org/garsa/). For download requests visit http://www.biowebdb.org/garsa/ or contact Dr Alberto Dávila.

Animals↗
PubMed2005

Intelligent client for integrating bioinformatics services.

MOTIVATION: In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem. RESULTS: In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Automation↗
PubMed2006

A reference database for circular dichroism spectroscopy covering fold and secondary structure space.

MOTIVATION: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.

Algorithms↗
PubMed2006

PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature.

SUMMARY: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. AVAILABILITY: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/.

Abstracting and Indexing↗
PubMed2006

Integration of gel-based proteome data with pProRep.

UNLABELLED: pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel. AVAILABILITY: The pProRep package and instructions for its use can be downloaded from http://www.ptools.ua.ac.be/pProRep. The application requires a web server that runs PHP 5 (http://www.php.net) and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.

Computational Biology↗
PubMed1996

Detection of short protein coding regions within the cyanobacterium genome: application of the hidden Markov model.

The gene-finding programs developed so far have not paid much attention to the detection of short protein coding regions (CDSs). However, the detection of short CDSs is important for the study of photosynthesis. We utilized GeneHacker, a gene-finding program based on the hidden Markov model (HMM), to detect short CDSs (from 90 to 300 bases) in a 1.0 mega contiguous sequence of cyanobacterium Synechocystis sp. strain PCC6803 which carries a complete set of genes for oxygenic photosynthesis. GeneHacker differs from other gene-finding programs based on the HMM in that it utilizes di-codon statistics as well. GeneHacker successfully detected seven out of the eight short CDSs annotated in this sequence and was clearly superior to GeneMark in this range of length. GeneHacker detected 94 potentially new CDSs, 9 of which have counterparts in the genetic databases. Four of the nine CDSs were less than 150 bases and were photosynthesis-related genes. The results show the effectiveness of GeneHacker in detecting very short CDSs corresponding to genes.

Algorithms↗
PubMed2025

TRAIT: A Comprehensive Database for T-cell Receptor-antigen Interactions.

Comprehensive and integrated resources on interactions between T-cell receptors (TCRs) and antigens are still lacking for adoptive T-cell-based immunotherapies, highlighting a significant gap that must be addressed to fully understand the mechanisms of antigen recognition by T cells. In this study, we present the T-cell receptor-antigen interaction database (TRAIT), a comprehensive database that profiles the interactions between TCRs and antigens. TRAIT stands out due to its comprehensive description of TCR-antigen interactions by integrating sequences, structures, and affinities. It provides millions of experimentally validated TCR-antigen pairs, resulting in an exhaustive landscape of antigen-specific TCRs. Notably, TRAIT emphasizes single-cell omics as a major reliable data source for TCR-antigen interactions and includes millions of reliable non-interactive TCRs. Additionally, it thoroughly demonstrates the interactions between mutations of TCRs and antigens, thereby benefiting affinity optimization of engineered TCRs as well as vaccine design. TCRs on clinical trials are innovatively provided. With the significant efforts made toward elucidating the complex interactions between TCRs and antigens, TRAIT is expected to ultimately contribute superior algorithms and substantial advancements in the field of T-cell-based immunotherapies. TRAIT is freely accessible at https://pgx.zju.edu.cn/traitdb.

Receptors, Antigen, T-Cell↗
PubMed2026

circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs.

Although extensive evidence has underscored the critical role of alternative splicing (AS) in generating mature circular RNA (circRNA) isoforms and augmenting their functional diversity, a significant gap remains in the availability of specialized databases housing circRNA AS events. To bridge this gap, we develop circASbase, a pioneering and comprehensive database that catalogs 452,129 AS events in 884,047 full-length circRNAs from 581 samples across 13 species, and provides rich annotations to facilitate understanding the splicing regulation of circRNA. Our findings reveal substantial differences between circRNAs and linear transcripts regarding the distribution and occurrence of AS events, highlighting the unique regulatory landscape of circRNAs. These special splicing events result in functional differences of circRNAs by affecting internal ribosome entry sites, N6-methyladenosine sites, open reading frames, protein features, microRNA targets, and more. In summary, circASbase not only meets the urgent need of the research community for data repositories, but also represents a significant advancement in our understanding of circRNA biology. With its user-friendly interfaces and web-based visualization tools, circASbase is poised to become an indispensable resource for researchers exploring the regulatory mechanisms and functional roles of AS events in circRNAs. This database will continuously drive new insights and discoveries in the field, setting the stage for further advancements in circRNA research. circASbase is freely available at http://reprod.njmu.edu.cn/cgi-bin/circASbase/.

Alternative Splicing↗
PubMed2005

Inherited occipital hypoplasia/syringomyelia in the cavalier King Charles spaniel: experiences in setting up a worldwide DNA collection.

Inherited diseases commonly emerge within pedigree dog populations, often due to use of repeatedly bred carrier sire(s) within a small gene pool. Accurate family records are usually available making linkage analysis possible. However, there are many factors that are intrinsically difficult about collecting DNA and collating pedigree information from a large canine population. The keys to a successful DNA collection program include (1) the need to establish and maintain support from the pedigree breed clubs and pet owners; (2) committed individual(s) who can devote the considerable amount of time and energy to coordinating sample collection and communicating with breeders and clubs; and (3) providing means by which genotypic and phenotypic information can be easily collected and stored. In this article we described the clinical characteristics of inherited occipital hypoplasia/syringomyelia (Chiari type I malformation) in the cavalier King Charles spaniel and our experiences in establishing a pedigree and DNA database to study the disease.

Animals↗
PubMed2005

Male-driven biased gene conversion governs the evolution of base composition in human alu repeats.

Regional biases in substitution pattern are likely to be responsible for the large-scale variation in base composition observed in vertebrate genomes. However, the evolutionary forces responsible for these biases are still not clearly defined. In order to study the processes of mutation and fixation across the entire human genome, we analyzed patterns of substitution in Alu repeats since their insertion. We also studied patterns of human polymorphism within the repeats. There is a highly significant effect of recombination rate on the pattern of substitution, whereas no such effect is seen on the pattern of polymorphism. These results suggest that regional biases in substitution are caused by biased gene conversion, a process that increases the probability of fixation of mutations that increase GC content. Furthermore, the strongest correlate of substitution patterns is found to be male recombination rates rather than female or sex-averaged recombination rates. This indicates that in addition to sexual dimorphism in recombination rates, the sexes also differ in the relative rates of crossover and gene conversion.

Alu Elements↗
PubMed2002

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein.

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The SYSTERS protein sequence cluster set provides an automatically generated classification of all sequences of the SWISS-PROT, TrEMBL and PIR databases into disjoint protein family and superfamily clusters. GeneNest is a database and software package for producing and visualizing gene indices from ESTs and mRNAs. Currently, the database comprises gene indices of human, mouse, Arabidopsis thaliana and zebrafish. SpliceNest is a web-based graphical tool to explore gene structure, including alternative splicing, based on a mapping of the EST consensus sequences from GeneNest to the complete human genome. The integration of SYSTERS, GeneNest and SpliceNest into one framework now permits an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. The databases are available for querying and browsing at http://cmb.molgen.mpg.de.

Alternative Splicing↗
PubMed2002

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

Amino Acid Sequence↗
PubMed2002

The KEGG databases at GenomeNet.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).

Animals↗
PubMed2002

RiceGAAS: an automated annotation system and database for rice genome sequence.

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Automation↗
PubMed2002

PipeOnline 2.0: automated EST processing and functional data sorting.

Expressed sequence tags (ESTs) are generated and deposited in the public domain, as redundant, unannotated, single-pass reactions, with virtually no biological content. PipeOnline automatically analyses and transforms large collections of raw DNA-sequence data from chromatograms or FASTA files by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant input files into a unigene EST data set and finally through translation, amino acid sequence similarity searches, annotation of public databases and functional data. PipeOnline generates an annotated database, retaining the processed unigene sequence, clone/file history, alignments with similar sequences, and proposed functional classification, if available. Functional annotation is automatic and based on a novel method that relies on homology of amino acid sequence multiplicity within GenBank records. Records are examined through a function ordered browser or keyword queries with automated export of results. PipeOnline offers customization for individual projects (MyPipeOnline), automated updating and alert service. PipeOnline is available at http://stress-genomics.org.

Automation↗
PubMed2003

Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003.

The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in genetics. This database is made for and by researchers and clinicians, who are encouraged to contribute. The Atlas is part of the genome project and it participates in research on cancer epidemiology.

Cytogenetic Analysis↗
PubMed2003

Enzyme-specific profiles for genome annotation: PRIAM.

The advent of fully sequenced genomes opens the ground for the reconstruction of metabolic pathways on the basis of the identification of enzyme-coding genes. Here we describe PRIAM, a method for automated enzyme detection in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices ('profiles') automatically tailored for each ENZYME entry. Automatically generated logical rules define which of these profiles is required in order to infer the presence of the corresponding enzyme in an organism. As an example, PRIAM was applied to identify potential metabolic pathways from the complete genome of the nitrogen-fixing bacterium Sinorhizobium meliloti. The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes.

Bacterial Proteins↗