The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motif...

Genome Surveyor 2.0 is a web-based tool for discovery and analysis of cis-regulatory elements in Drosophila, built on top of the GBrowse genome browser for convenient visualization. Genome Surveyor was developed as a tool for predicting transcription factor (TF) binding targets and cis-regulatory modules (CRMs/enhancers), based on motifs representing experimentally determined DNA binding specif...

The number of sequences from both formally described taxa and uncultured environmental DNA deposited in the International Nucleotide Sequence Databases has increased substantially over the last two decades. Although the majority of these sequences represent authentic gene copies, there is evidence of DNA artifacts in these databases as well. These include lab artifacts, such as PCR chimeras, an...

Functional turnover of transcription factor binding sites (TFBSs), such as whole-motif loss or gain, are common events during genome evolution. Conventional probabilistic phylogenetic shadowing methods model the evolution of genomes only at nucleotide level, and lack the ability to capture the evolutionary dynamics of functional turnover of aligned sequence entities. As a result, comparative ge...

Background: Cytotoxin-associated gene A (CagA)-positive strains of Helicobacter pylori are associated with gastroduodenal diseases. Evidences have suggested that the type of H pylori CagA EPIYA motifs may be associated with specific disorders (i.e., gastritis, peptic ulcer, or gastric cancer).  We investigated the prevalence of different EPIYA motifs (A, B, C, or D) in H. pylori strains is...

Suboptimal light stress in grapevines is increasing worldwide with the spread of grapevine cultivation, which can affect physiology and productivity, such as Southern China. Abscisic acid (ABA) an important hormone plant adaptive responses to abiotic stress, including low stress. However, ABA signaling pathway genes (APGs) are not well characterized grapevine, little known their potentially mit...

Small ubiquitin-related modifier (SUMO) is a post-translational modification factor composed of about 100 amino acid residues. Most plant species express family SUMO isoforms. We found three novel homologs rice (Oryza sativa L.) genes, OsSUMO4, OsSUMO5 and OsSUMO6, in addition to the known genes OsSUMO1–OsSUMO3. Phylogenetic tree analysis revealed that have diverged considerably during their ev...

NAC proteins, part of the largest plant transcription factor family, play pivotal roles in development, and biotic abiotic stresses. Among them, SlNAC1 protein tomato serves as a Negative regulator, enhancing tolerance to cold, bacterial, viral diseases. However, our knowledge silico analysis, evolutionary relationships, interactions remains limited. We used tools study tomato. Phylogenetic ana...

quorum sensing controls the luminescence of vibrio fischeri through the transcriptional activator luxr and the specific autoinducer signal produced by luxi. amino acid sequences of these two genes were analyzed using bioinformatics tools. luxi consists of 193 amino acids and appears to contain five α-helices and six ß-sheets when analyzed by sspro8. luxi belongs to the autoinducer synthetase fa...