BIOFFORC: tool development for biological file format conversion.

UNLABELLED: The use of bioinformatics tools require different sequence formats at various instances. Every tool uses specific set of formats for processing. Sequence in one format is often required in another format. Thus, there is a need for sequence format conversion. A number of such tools are available in the public domain. Here, we describe BIOFFORC as a file format converter. The tool is developed with a graphical user interface in PERL. AVAILABILITY: http://www.winningpath.com/biofforc/

Background

The basic format underling information in DDBJ/EMBL/GenBank is a flat file. The correspondence between individual flat file formats facilitated the exchange of data between each of these datasets [1]. GenBank describes each sequence entry with literature reference, functional data, location of mRNA coding regions and sequence [2]. Similarly, EMBL [3] and DDBJ [4] are also resources for biological and medical research data. The sequence file format conversion with tools like READSEQ [5], FMTSEQ [6] and SeqVerter [7] are described in detail. Here, we describe BIOFFORC as a file format converter.

Methodology

Process flow

A process flow for the tool is shown in Figure 1.

Figure 1

Process flow diagram for BIOFFORC tool

Web interface

The current version of BIOFFORC is a web based tool and it uses a common gateway interface (CGI) developed in PERL.

Input and output

The use of the tool to convert a GenBank format to FASTA format is shown in Figure 2. The top panel in Figure 2 shows input in GenBank Format and the bottom panel shows output in FASTA format.

Figure 2

Sample input and output for and from BIOFFORC is shown

Caveats and Future development

The present version of BIOFFORC allows format conversion for four formats. We propose to expand conversion capability to several other required formats.