Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Centre For Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012 ,Anu Sharma,SB Lal,Anil Rai

doi:10.6026/97320630009663

Centre For Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012 , Anu Sharma

Open Access

https://doi.org/10.6026/97320630009663

Copy DOI

Abstract

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.

Highlights

MODERN biology is driven by large scale processing of heterogeneous data, which may come from diverse sources, such as sequences from GenBank, EMBL, PDB, DDJB, PROSITE, NGS and many other secondary databases
There is an urgent need for development of solutions for integration of various tools and database to assist biologist from burden on executing them independently on different platforms
This article attempt to compare the features and performance of workflows developed for gene sequence analysis and evolutionary studies

Summary

Background

MODERN biology is driven by large scale processing of heterogeneous data, which may come from diverse sources, such as sequences from GenBank, EMBL, PDB, DDJB, PROSITE, NGS and many other secondary databases. Workflow Management System (WMS) is the integration of several bioinformatics tools with multiple databases, to automate the analysis and storage of genomic sequences. Several WMSs were developed for researchers to perform computational analysis with ease using various computational tools These workflow systems, differs in scope and approach of integration for their execution. Many of these WMS are available as web based servers to provide access to powerful computing resources through familiar graphical-based environment for inexperienced users. Protein Annotation Toolkit (PAT) [6] is an integrated bio-computing server that provides a standardized web interface to a wide range of protein analysis tools It is designed as a streamlined analysis environment that implements many features, which strongly simplify studies dealing with protein sequences/structures and improve productivity.

Conclusion

Common Link

Aligns and merges sequence fragments

GENOMESCA N ATGpr

PAT PIPA AFAWE

It is written in CGI and PERL

Multiple Sequence Alignment

Phylogenetic Tree Inference

Maximum likelihood and statistical analysis

Linux e

Phylogenetic Tree Visualization

Implementati Tools Used on Phylogena Phylemon