About BBProF (An Asynchronous Bacterial Bioleaching Protein Finder)


General Information

BBProF is a web server developed to identify potential bioleaching bacteria from their whole genome sequences. BBProF rapidly predicts putative bacterial proteins involved in the underlying iron and sulphur oxidation pathways and performs phylogenomic analysis of 16s rRNA genes to determine the evolutionary relationship between the organisms. The server uses the features of Asynchronous Java Script and XML (AJAX) and in the input form accepts any bacterial genome sequence in RAW format to provide the list of proteins involved in bioleaching as output. BBProF web server is integrated with the European Bioinformatics Institute (EBI) web services such as BLAST for homology search and InterProScan for functional characterization of output protein sequences. Complete genome sequences of 24 experimentally known bioleaching bacterial strains and their respective 16S rRNA gene sequences were stored in the database of BBProF library. Studying of evolutionary relationship of bacterial strains of interest using Muscle and ClustalW2 phylogeny web services from EBI is another key feature of our server.

  • Protein Finder

    The Protein Finder Module of BBProF implements the pattern-matching protocol to predict putative proteins involved in bioleaching from the whole genome sequence of the input bacterial strain. Consensus patterns of proteins involved in iron- and/or sulfur-oxidation electron transfer pathways of bioleaching bacteria were either collected from Prosite or constructed manually using PRATT program. These retrieved conserved residual patterns were stored in the BBProF database library. An integrated ORF finder program in BBProF, identifies and subsequently translates protein coding regions from the input bacterial complete genome sequence. The resulting amino acid sequences are then matched with the corresponding patterns stored in the BBProF library. If a pattern is found in the input sequence, the server correctly predicts it as a putative protein with bioleaching efficiency. To further corroborate the results, predicted proteins are additionally subjected to BLAST and InterProScan analysis which are integrated into our server for a pipeline workflow.

    Click Here to see Flow Chart of Protein Finder

  • Phylogenetic Analysis

    In order to gain insights into evolutionary relationship of the bacterial bioleaching microbes, a simple and easy-to-use phylogenetic analysis module has been integrated with the web server. Based on bacterial 16S rRNA sequences this module constructs a phylogenetic tree of the query bacterium with the experimentally reported bioleaching organisms. Multiple sequence alignment and phylogenetic tree are determined using MUSCLE and ClustaW2 phylogeny programs, respectively.

    Click Here to see Flow Chart of Phylogenetic Analysis