1. Protein Finder Module
    • Submit a job
    • Retrieve Results
  2. Phylogenetic Analysis
    • Submit a Job
    • MSA (Multiple Sequence Alignment) result
    • Phylogenetic Tree

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. The work flow of the Protein Finder module is as follows:

  1. Submit a job
    Input interface for this module is provided from the home page. A simple text area is provided where user is required to paste any bacterial whole genome sequence in RAW format. Further, to provide the user with instant access to genome data of experimentally known bioleaching bacteria, we have stored complete genome sequences of 24 well known acidophilic/thermophilic bacterial strains in BBProF database library which can be accessed from a dropdown menu, provided just below the input box. (Click here to view)
  2. Retrieve Result
    The output of the protein finder module displays a well-organized web-page with the following results: (i) GC content of the entire genome; (ii) a list of putative proteins involved in the electron transfer pathway during iron- and sulfur-oxidation along with their consensus conserved patterns, hyperlinks for Prosite entry and documentation ID, amino acid sequences and hyperlinks for in-built BLASTp and InterProScan modules; (iii) the time elapsed by the protein finder module; (iv) an indicator in graphical form with 'high', 'medium' or 'low' potential of the bacteria for iron- and sulfur-oxidation depending on the total number of the identified proteins found from the input bacterial genome sequence. (Click here to view).

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.

  1. Submit a job
    The phylogenetic analysis module accepts 16S rRNA genes of bacteria as user input from the following 3 different JQUERY-based options : (i) Input from database - BBProF database library has stored 16S rRNA genes of 24 bioleaching bacterial strains. Input source of 16S rRNA gene sequences may be from one or more number of bacterial strains which the user has to select for further analysis; (Click here to view) (ii) Direct input - here the user can provide input sequence of 16S rRNA gene of any bacterial strain(Click here to view), and (iii) Input through in-silico PCR amplification - this option is especially useful when the 16S rRNA genes of the bacterium is not available and therefore, the required amplification is carried out in silico(Click here to view). A program for PCR amplification has been coded considering two universally used primers for bacterial 16S rRNA gene. The result displays a list of amplicons that can be stored to temporary memory for subsequent phylogenetic analysis.

  2. MSA (Multiple Sequence Result)result
    For multiple sequence alignment of the input query sequences, MUSCLE program of EBI (The European Bioinformatics Institute) has been integrated with the web server (Click here to view).

  3. Phylogenetic tree
    The output of phylogenetic analysis module is displayed on a single page along with branch length values. Phylogenetic trees can be constructed in various formats like unrooted, phenogram, curvogram, eurogram, swoopogram and circular tree, using the integrated ClustalW2 program of EBI.Click here to view).