BMC Bioinformatics - Volume 8, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

Integration of multiple results from Quantitative Trait Loci (QTL) studies is a key point to understand the genetic determinism of complex traits. Up to now many efforts have been made by public database developers to facilitate the storage, compilation and visualization of multiple QTL

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at th

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and th

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been widely used to investigate the DNA binding sites for a variety of proteins on a genome-wide scale. However, several issues in the processing and analysis of ChIP-chip data have not been resolved fully, including the eff

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisi

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Metabolic Flux Analysis (MFA) based on isotope labeling experiments (ILEs) is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs) contain all essential information required to describe the flow of labeled material in an ILE. Whereas r

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites.

Results

We have

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (mRNA) level in both eukaryotic and prokaryotic systems and are thus

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007

Abstract

Background

With the advent of increasing sequence and structural data, a number of methods have been proposed to locate putative protein binding sites from protein surfaces. Therefore, methods that are able to identify whether these binding sites interact are needed.

Results

We have developed

Journal: BMC Bioinformatics, vol. 8, no. Preprint, 2007