BMC Bioinformatics - Volume 9, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, i

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

Various measures of semantic similarity of terms in bio-ontologies such as the Gene Ontology (GO) have been used to compare gene products. Such measures of similarity have been used to annotate uncharacterized gene products and group gene products into functional groups. There are vario

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

Modern sequencing technologies allow rapid sequencing and bioinformatic analysis of genomes and metagenomes. With every new sequencing project a vast number of new proteins become available with many genes remaining functionally unclassified based on evidences from sequence similarities

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

Outer membrane proteins (OMPs) perform diverse functional roles in Gram-negative bacteria. Identification of outer membrane proteins is an important task.

Results

This paper presents a method for distinguishing outer membrane proteins (OMPs) from non-OMPs (that is, globular protein

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data is to perform cluster analysis. While many clustering algorithms have been deve

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

Detecting conserved noncoding sequences (CNSs) across species highlights the functional elements. Alignment procedures combined with computational prediction of transcription factor binding sites (TFBSs) can narrow down key regulatory elements. Repeat masking processes are often perform

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries.

Results

Using sequence information obtained from GenB

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and t

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008

Abstract

Background

The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matr

Journal: BMC Bioinformatics, vol. 9, no. Preprint, 2008