RSMD-repeat searcher and motif detector

The functionality of a gene or a protein depends on codon repeats occurring in it.As a consequence of their vitality in protein function and apparent involvement in causing diseases,an interest in these repeats has developed in recent years.The analysis of genomic and proteomic sequences to identify such repeats requires some algorithmic support from informatics level.Here,we proposed an offline stand-alone toolkit Repeat Searcher and Motif Detector（RSMD）,which uncovers and employs few novel approaches in identification of sequence repeats and motifs to understand their functionality in sequence level and their disease causing tendency.The tool offers various features such as identifying motifs,repeats and identification of disease causing repeats.RSMD was designed to provide an easily understandable graphical user interface（GUI）,for the tool will be predominantly accessed by biologists and various researchers in all platforms of life science.GUI was developed using the scripting language Perl and its graphical module PerlTK.RSMD covers algorithmic foundations of computational biology by combining theory with practice.

Genomics and proteomics of Apis mellifera filamentous virus isolated from honeybees in China

Apis mellifera filamentous virus(Am FV)is a large DNA virus that is endemic in honeybee colonies.The genome sequence of the Am FV Swiss isolate(Am FV CH–C05)has been reported,but so far very few molecular studies have been conducted on this virus.In this study,we isolated and purified Am FV(Am FV CN)from Chinese honeybee(Apis mellifera)colonies and elucidated its genomics and proteomics.Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm,wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops.Unlike Am FV CH–C05,which was reported to have a circular genome,our data suggest that Am FV CN has a linear genome of approximately 493 kb.A total of 197 ORFs were identified,among which36 putative genes including 18 baculoviral homologs were annotated.The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%.Several ORFs were newly annotated in Am FV CN,including homologs of per os infectivity factor 4(PIF4)and a putative integrase.Phylogenomic analysis placed Am FVs on a separate branch within the newly proposed virus class Naldaviricetes.Proteomic analysis revealed 47 Am FV virionassociated proteins,of which 14 had over 50%sequence coverage,suggesting that they are likely to be main structural proteins.In addition,all six of the annotated PIFs(PIF-0–5)were identified by proteomics,suggesting that they may function as entry factors in Am FV infection.This study provides fundamental information regarding the molecular biology of Am FV.