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BACKGROUND Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also(More)
BACKGROUND Shine-Dalgarno (SD) signal has long been viewed as the dominant translation initiation signal in prokaryotes. Recently, leaderless genes, which lack 5'-untranslated regions (5'-UTR) on their mRNAs, have been shown abundant in archaea. However, current large-scale in silico analyses on initiation mechanisms in bacteria are mainly based on the(More)
MOTIVATION A high-quality assembly of reads generated from shotgun sequencing is a substantial step in metagenome projects. Although traditional assemblers have been employed in initial analysis of metagenomes, they cannot surmount the challenges created by the features of metagenomic data. RESULT We present a de novo assembly approach and its(More)
Ethylene has been regarded as a stress hormone to regulate myriad stress responses. Salinity stress is one of the most serious abiotic stresses limiting plant growth and development. But how ethylene signaling is involved in plant response to salt stress is poorly understood. Here we showed that Arabidopsis plants pretreated with ethylene exhibited enhanced(More)
BACKGROUND Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relationship. However, at present, the prediction accuracy of pure HMM-type methods is much lower than that of machine learning-based methods such(More)
MOTIVATION At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3' end), but a much lower accuracy of the translation initiation site (TIS, 5' end). The latter is important to the analysis and the understanding of the putative protein of a gene and the(More)
BACKGROUND As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated(More)
UNLABELLED We report a new and simple method, TriTISA, for accurate prediction of translation initiation site (TIS) of microbial genomes. TriTISA classifies all candidate TISs into three categories based on evolutionary properties, and characterizes them in terms of Markov models. Then, it employs a Bayesian methodology for the selection of true TIS with a(More)
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for(More)
A new simple method is found for efficient and accurate identification of coding sequences in prokaryotic genome. The method employs a Shannon description of artificial language for DNA sequences. It consists in translating a DNA sequence into a pseudo-amino acid sequence with 20 fundamental words according to the universal genetic code. With an(More)