Literature DB >> 33961228

A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists.

Camilla Fagorzi1, Alice Checcucci2.   

Abstract

Making use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data.

Keywords:  Bacteria; Bioinformatics; Genomics; Wet lab

Year:  2021        PMID: 33961228     DOI: 10.1007/978-1-0716-1099-2_15

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  18 in total

1.  GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.

Authors:  Bruno Contreras-Moreira; Pablo Vinuesa
Journal:  Appl Environ Microbiol       Date:  2013-10-04       Impact factor: 4.792

2.  Prokka: rapid prokaryotic genome annotation.

Authors:  Torsten Seemann
Journal:  Bioinformatics       Date:  2014-03-18       Impact factor: 6.937

3.  The integrated microbial genome resource of analysis.

Authors:  Alice Checcucci; Alessio Mengoni
Journal:  Methods Mol Biol       Date:  2015

4.  panX: pan-genome analysis and exploration.

Authors:  Wei Ding; Franz Baumdicker; Richard A Neher
Journal:  Nucleic Acids Res       Date:  2018-01-09       Impact factor: 16.971

5.  Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.

Authors:  Chad Laing; Cody Buchanan; Eduardo N Taboada; Yongxiang Zhang; Andrew Kropinski; Andre Villegas; James E Thomas; Victor P J Gannon
Journal:  BMC Bioinformatics       Date:  2010-09-15       Impact factor: 3.169

6.  PGAP: pan-genomes analysis pipeline.

Authors:  Yongbing Zhao; Jiayan Wu; Junhui Yang; Shixiang Sun; Jingfa Xiao; Jun Yu
Journal:  Bioinformatics       Date:  2011-11-29       Impact factor: 6.937

7.  MetaRef: a pan-genomic database for comparative and community microbial genomics.

Authors:  Katherine Huang; Arthur Brady; Anup Mahurkar; Owen White; Dirk Gevers; Curtis Huttenhower; Nicola Segata
Journal:  Nucleic Acids Res       Date:  2013-11-06       Impact factor: 16.971

8.  Roary: rapid large-scale prokaryote pan genome analysis.

Authors:  Andrew J Page; Carla A Cummins; Martin Hunt; Vanessa K Wong; Sandra Reuter; Matthew T G Holden; Maria Fookes; Daniel Falush; Jacqueline A Keane; Julian Parkhill
Journal:  Bioinformatics       Date:  2015-07-20       Impact factor: 6.937

9.  CD-HIT: accelerated for clustering the next-generation sequencing data.

Authors:  Limin Fu; Beifang Niu; Zhengwei Zhu; Sitao Wu; Weizhong Li
Journal:  Bioinformatics       Date:  2012-10-11       Impact factor: 6.937

10.  BPGA- an ultra-fast pan-genome analysis pipeline.

Authors:  Narendrakumar M Chaudhari; Vinod Kumar Gupta; Chitra Dutta
Journal:  Sci Rep       Date:  2016-04-13       Impact factor: 4.379

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