Short well-defined domains known as peptide recognition modules (PRMs) regulate many important protein-protein interactions involved in the formation of macromolecular complexes and biochemical pathways. High-throughput experiments like yeast two-hybrid and phage display are expensive and intrinsically noisy, therefore it would be desirable to target informative interactions and pursue in silic...

The Indian stingless bee Tetragonula iridipennis (Hymenoptera: Apidae), popularly recognized as the dammer bee, is an economically important and widely distributed non- Apis species in India. taxonomic gaps, systematics, evolutionary puzzles, structural motifs within mitogenomes of this have rarely been examined are not fully understood. Next-generation sequencing was employed to decipher compl...

decorative arts have got a special place in iranian architecture traditionally. these types of arts are the symbol of nation's ethnics and indigenous features and also express the artist's feelings of those times. stucco is one type of the decorative arts that has decorated many buildings -especially palaces-that belong to the pre-islamic period and also mosques that built in the isla...

A large set of candidate nucleotide-binding site (NBS)-encoding genes related to disease resistance was identified in the sorghum (Sorghum bicolor) genome. These resistance (R) genes were characterized based on their structural diversity, physical chromosomal location and phylogenetic relationships. Based on their N-terminal motifs and leucine-rich repeats (LRR), 50 non-regular NBS genes and 22...

iran is a large country with a vast variety of tribes and ethnic groups. these various tribes are unified with a national language and culture while using their own local languages and enriching ethnic art forms. among iranian ethnic groups, the turkmen are remarkable for their art of carpet weaving which has a unique structure compared to other designs and textures. the charming motifs on turk...

FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment bl...

ADP-glucose pyrophosphorylase (AGPase), a key enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Ample evidence has shown that the AGPase catalyzes the rate limiting step in starch biosynthesis in higher plants. In this study, we compiled detailed comparative information about ADP glucose pyrophosphorylase in selected plants by analy...

Using comparative genomics approaches, we analyzed the regulation of ribonucleotide reductase genes in bacterial genomes. A highly conserved palindromic signal with consensus acaCwAtATaTwGtg, named NrdR-box, was identified upstream of most operons encoding ribonuleotide reductases from three different classes. By correlating the occurrence of NrdR-boxes with phylogenetic distribution of ortholo...

MOTIVATION Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications of local alignment algorithms (e.g. phylogenetic footprinting) would benefit from including prior knowledge (e.g. binding site motifs) in the alignment building process. RESULTS We introduce predefi...