BMC Bioinformatics - Volume 6, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility to evaluate multiple sources of variation in an experiment.

Results

AnovAr

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

With microarray technology the expression of thousands of genes can be measured simultaneously. It is well known that the expression levels of genes of interacting proteins are correlated significantly more strongly in Saccharomyces cerevisiae than those of proteins that are not

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objective was to establish an automated text-mining system for OMIM that will ident

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and inte

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

This paper describes SeqDoC, a simple, web-based tool to carry out direct comparison of ABI sequence chromatograms. This allows the rapid identification of single nucleotide polymorphisms (SNPs) and point mutations without the need to install or learn more complicated analysis software.

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related g

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

Evolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignment accuracy of DNA sequences on evolutionary distance estimation.

Results

Under the studied conditions, distance est

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005

Abstract

Background

One of the primary tasks in analysing gene expression data is finding genes that are differentially expressed in different samples. Multiple testing issues due to the thousands of tests run make some of the more popular methods for doing this problematic.

Results

We propose a simpl

Journal: BMC Bioinformatics, vol. 6, no. Preprint, 2005