During the bacterial cell cycle, the processes of chromosome replication, DNA segregation,
DNA repair and cell division are coordinated by precisely defined events. Tremendous …

The two-component signal transduction system BarA-UvrY of Escherichia coli and its
orthologs globally regulate metabolism, motility, biofilm formation, stress resistance …

Motivation Motif identification and analyses are important and have been long-standing
computational problems in bioinformatics. Substantial efforts have been made in this field …

Achromobacter denitrificans is an environmental opportunistic pathogen that is infecting a
large number of immunocompromised patients. A more recently identified strain from the …

Finding significant nucleotide sequence motifs in prokaryotic genomes can be divided into
three types of tasks:(1) supervised motif finding, where a sample of motif sequences is used …

The σ54 regulon in Salmonella enterica serovar Typhimurium includes a predicted RNA
repair operon encoding homologs of the metazoan Ro60 protein (Rsr), Y RNAs (YrlBA) …

The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which
is responsible for promoter specificity and open complex formation, plays a strategic role in …

The Sac10b protein family, also known as Alba, is widely distributed in Archaea. Sac10b
homologs in thermophilic Sulfolobus species are very abundant. They bind both DNA and …

Background Interactions between transcription factors and their specific binding sites are a
key component of regulation of gene expression. Until recently, it was generally assumed …

Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide
composition as well as presence of various sequence features that can affect physical …