ATP(CTP):tRNA nucleotidyl transferases, tRNA maturing enzymes found in all organisms, and eubacterial poly(A) polymerases, enzymes involved in mRNA degradation, are so similar that until now their biochemical functions could not be distinguished by their amino acid sequence. BLAST searches and analysis with the program "Sequence Space" for the prediction of functional residues revealed sequence...

DivergentSet addresses the important but so far neglected bioinformatics task of choosing a representative set of sequences from a larger collection. We found that using a phylogenetic tree to guide the construction of divergent sets of sequences can be up to 2 orders of magnitude faster than the naive method of using a full distance matrix. By providing a user-friendly interface (available onl...

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3'-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential r...

Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting ...

Low phosphorus increases acid phosphatase activity and transfers soluble from the underground to above-ground, but also inhibits growth development of Moso bamboo root system. Purple (PAP), a kind phosphatase, plays an important role in (P) uptake metabolism. In our study PAP gene family, we identified 17 genes (PePAP) entire genome further analyzed their physical chemical properties functions ...

Peroxidases (PODs) have various physiological and biochemical roles in plant growth, development stress response. The POD genes were identified species, but passion fruit has not yet been thoroughly characterized. Here, we discovered 30 putative from the genome of Passiflora edulis Sims. For further elucidation, comprehensive bioinformatics analysis was utilized to determine physicochemical pro...

A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. ...

Abstract Background Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that widely found in plants and animals, the second largest factor family eukaryotes after MYB. They have been shown to be important regulatory components tissue development many different biological processes. However, no systemic analysis bHLH has yet reported Sorghum bicolor . Results We conducted fir...

Motivation The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting ...

Background: Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif p...