MEGA biocentric software for sequence and phylogenetic analysis: a review

Biocomputing has moved into central position in molecular biology research. Enormous improvements in genetic engineering have led to the accumulation of a vast amount of biological information. With the advent of this extensive repertoire of raw sequence information, the next major challenge for a modern researcher is to interpret this biological information. Molecular Evolutionary Genetic Analysis (MEGA) is bio-computational software to fill the vacuum between data development and analysis. In this paper, an attempt to review the evolution of MEGA software, working and application has been made. Moreover, data analysis, implementation and advantages over other bioinformatics software have been discussed systematically.

[1]  Shawn Hoon,et al.  Biopipe: a flexible framework for protocol-based bioinformatics analysis. , 2003, Genome research.

[2]  Joel Dudley,et al.  MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences , 2008, Briefings Bioinform..

[3]  Mark Borodovsky,et al.  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses , 2005, Nucleic Acids Res..

[4]  Gary D. Bader,et al.  cPath: open source software for collecting, storing, and querying biological pathways , 2006, BMC Bioinformatics.

[5]  Giancarlo Mauri,et al.  Biowep: a workflow enactment portal for bioinformatics applications , 2007, BMC Bioinformatics.

[6]  Gajendra P. S. Raghava,et al.  OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy , 2003, BMC Bioinformatics.

[7]  Daniel N. Frank,et al.  XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data , 2008, BMC Bioinformatics.

[8]  Stefan Schuster,et al.  YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities , 2005, BMC Bioinformatics.

[9]  Tao Xu,et al.  Pegasys: software for executing and integrating analyses of biological sequences , 2004, BMC Bioinformatics.

[10]  Elarbi Badidi,et al.  AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis , 2003, BMC Bioinformatics.

[11]  Brian Fristensky,et al.  BIRCH: A user-oriented, locally-customizable, bioinformatics system , 2007, BMC Bioinformatics.

[12]  Jake Yue Chen,et al.  ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining , 2008, BMC Bioinformatics.

[13]  Chuan Yi Tang,et al.  RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints , 2007, Nucleic Acids Res..

[14]  Erik L. L. Sonnhammer,et al.  Kalign – an accurate and fast multiple sequence alignment algorithm , 2005, BMC Bioinformatics.

[15]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[16]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[17]  David J. Reiss,et al.  The Gaggle: An open-source software system for integrating bioinformatics software and data sources , 2006, BMC Bioinformatics.

[18]  Egon L. Willighagen,et al.  Bioclipse: an open source workbench for chemo- and bioinformatics , 2007, BMC Bioinformatics.

[19]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[20]  Priyanka Gupta,et al.  BioWarehouse: a bioinformatics database warehouse toolkit , 2006, BMC Bioinformatics.

[21]  Monica C. Sleumer,et al.  Sockeye: a 3D environment for comparative genomics. , 2004, Genome research.

[22]  Ezio Bartocci,et al.  BioWMS: a web-based Workflow Management System for bioinformatics , 2007, BMC Bioinformatics.

[23]  Tao Xu,et al.  Atlas – a data warehouse for integrative bioinformatics , 2005, BMC Bioinformatics.

[24]  Forest Rohwer,et al.  FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries , 2006, BMC Bioinformatics.

[25]  Scot E. Dowd,et al.  Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST) , 2005, BMC Bioinformatics.

[26]  Thomas Soddemann,et al.  The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis , 2006, Nucleic Acids Res..