Biospectrogram: a tool for spectral analysis of biological sequences

TL;DR

Biospectrogram is an open-source Java tool that enables spectral analysis of biological sequences using DSP techniques, supporting data fetching, encoding, transformation, and MATLAB export for advanced analysis.

Contribution

It introduces a versatile software platform for spectral analysis of DNA and protein sequences with multiple encoding options and MATLAB integration, enhancing biological data analysis capabilities.

Findings

Supports 23 encodings for biological sequences.

Allows dynamic spectral pattern search with MATLAB.

Compatible across Windows, Mac OSX, and Linux.

Abstract

Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing (DSP) techniques since the software allows the user to convert the symbolic data into numerical data using 23 popular encodings and then apply popular transformations such as Fast Fourier Transform (FFT) etc. and export it. The ability of exporting (both encoding files and transform files) as a MATLAB .m file gives the user an option to apply variety of techniques of DSP. User can also do window analysis (both sliding in forward and backward directions and stagnant) with different size windows and search for meaningful spectral pattern with the help of exported MATLAB file in a dynamic manner by choosing time delay in the plot using Biospectrogram. Random encodings and user choice encoding allows software to search for many possibilities in spectral space. Availability: Biospectrogam is written in Java and is available to download freely from http://www.guptalab.org/biospectrogram. Software has been optimized to run on Windows, Mac OSX and Linux. User manual and you-tube (product demo) tutorial is also available on the website. We are in the process of acquiring open source license for it.