Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide info...

The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures, http://pints.embl.de) performs database ...

With the advent of comparative genomics, an increasing amount of genomic data from different organisms is to be compared. This paper presents an approach to integrate bioinformatics data from various source databases using web services and a private registry. The goal is to construct an efficient framework that correctly integrates genomic databases via web services and thus allows genomic brow...

The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics. To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome sequences and are widely accessible to the scientific...

This paper demonstrates that a large-scale lexicon tailored for the biology domain is effective in improving question analysis for genomics Question Answering (QA). We use the TREC Genomics Track data to evaluate the performance of different question analysis methods. It is hard to process textual information in biology, especially in molecular biology, due to a huge number of technical terms w...

In this paper, an overview of the main topics presented in the special session of bioinformatics and biomedical engineering is presented. Bioinformatics consists of two subfields: the development of computational tools and databases, and the application of these tools and databases in generating biological knowledge to better understand living systems, being the main subject genomics and proteo...

The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgroun...

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, inclu...

In this article, a new approach is proposed for the de novo protein sequencing problem. The aim is to find the sequence of an experimental protein from only experimental data i.e. without databases. To do so, a three-step model called SSO for Shape, Sequence and Order has been designed. No prior knowledge in genomics nor protein databases are used. Here we modelize de novo protein sequencing as...

to compare different qtl mapping methods, a population with genotypic and phenotypic data was simulated. in bayesian approach, all information of markers can be used along with combination of distributions of snp markers. it is assumed that most of the markers (95%) have minor effects and a few numbers of markers (5%) exert major effects. the simulated population included a basic population of ...