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IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Muhammad Tariq Pervez1, Masroor Ellahi Babar2, Asif Nadeem3

  • 1Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.

Evolutionary Bioinformatics Online
|April 11, 2015
PubMed
Summary

IVisTMSA is a powerful software package for multiple sequence alignments, offering enhanced data handling and efficient analysis tools. It significantly outperforms existing software in speed and data capacity for critical bioinformatics tasks.

Keywords:
FASTAMSA Identity MatrixMSA comparatorMSA editing tool

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is fundamental in bioinformatics for understanding protein and nucleic acid sequence relationships.
  • Existing MSA tools often face limitations in data handling capacity and analysis speed.
  • Efficient visualization and analysis of large-scale alignments are crucial for modern biological research.

Purpose of the Study:

  • To introduce IVisTMSA, a novel software package comprising seven graphical tools for advanced multiple sequence alignment analysis.
  • To provide users with efficient and scalable tools for editing, comparing, reconstructing, and analyzing large sequence datasets.
  • To enhance the speed and data capacity of common bioinformatics workflows related to sequence alignment.

Main Methods:

  • IVisTMSA integrates seven distinct graphical tools: MSApad, MSA comparator, MSA reconstruction, FASTA generator, MSA ID calculator, Tree calculator, and Distance Matrix calculator.
  • MSApads offers superior data loading capacity compared to Jalview, STRAP, CINEMA, and Base-by-Base.
  • MSA comparator achieves high efficiency in visualizing large alignments (>21 MB) rapidly.
  • MSA reconstruction provides a user-friendly interface for popular aligners, supporting batch processing.
  • FASTA generator converts multiple alignment formats to FASTA swiftly.
  • MSA ID calculator processes extensive datasets (>11,000 sequences) rapidly.
  • Tree and Distance Matrix tools generate phylogenetic data using standard algorithms.

Main Results:

  • MSApads demonstrates a 409% increase in data loading capacity over existing tools.
  • MSA comparator is over 5,200% more efficient than BALiBASE c and over 40% more efficient than FastSP for large alignment comparisons.
  • The FASTA generator handles unlimited-sized alignments and converts formats in seconds.
  • The MSA ID calculator computes identity matrices for over 11,000 sequences in under 100 seconds.
  • Phylogenetic trees and distance matrices are generated efficiently.

Conclusions:

  • IVisTMSA provides a comprehensive and highly efficient suite of tools for multiple sequence alignment analysis.
  • The software significantly improves upon existing tools in terms of speed, data handling, and user interface.
  • IVisTMSA is a valuable resource for researchers requiring robust and scalable solutions for large-scale sequence data analysis in bioinformatics and genomics.