the earliest evidences on circulation of avian influenza (ai) virus on the iranian poultry farms date back to 1998. great economic losses through dramatic drop in egg production and high mortality rates are characteristically attributed to h9n2 ai virus. in the present work non-structural (ns) genes of 10 iranian h9n2 chicken ai viruses collected during 1998-2007 were fully sequenced and subjec...

Phylogenetic profiling involves the study of the occurrence of gene families across fully sequenced genomes. For any gene, it is possible to create a phylogenetic profile which encodes the presence or absence of homologs of the gene across organisms. The comparison of phylogenetic profiles may be used to measure the evolutionary distance between organisms leading to the reconstruction of phylog...

MOTIVATION Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. RESULTS We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP...

Protein banding pattern of eight snakeheads – Channa species viz., Channa striatus, Channa marulius, Channa punctatus, Channa diplogramme, Channa bleheri, Channa gachua, Channa stewartii and Channa aurantimaculata collected from different regions of India were used to study the phylogenetic relationship among them. The banding pattern from muscle protein indicated a unique profile for each spec...

Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins. We present a new method for finding such relations based on phylogenetic profiling of conserved domains rather than proteins, avoiding computationally expensive all versus all sequence comparisons among genomes. The resulting domain interaction map (DIMA) can be ex...

Phylogenetic profiling involves the comparison of phylogenetic data across gene families. It is possible to construct phylogenetic trees, or related data structures, for specific gene families using a wide variety of tools and approaches. Phylogenetic profiling involves the comparison of this data to determine which families have correlated or coupled evolution. The underlying assumption is tha...

The concept of modularity assumes that functionality can be partitioned into a collection of modules. Each module is a discrete entity of elementary components and performs an identifiable task, separable from the functions of other modules [3]. As the modules in the protein 3D structure can be related to molecular functions, the modules in the protein network may be related to cellular functio...