Phamerator: a bioinformatic tool for comparative bacteriophage genomics

BMC Bioinformatics
Steven G CresawnGraham F Hatfull

Abstract

Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation. We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange. Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.

References

Oct 25, 1975·Journal of Molecular Biology·M M Susskind, D Botstein
Jul 1, 1993·Molecular Microbiology·D L WulffM Rosenberg
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·W N Grundy
Dec 10, 1998·Nucleic Acids Research·A BatemanE L Sonnhammer
Mar 3, 1999·Proceedings of the National Academy of Sciences of the United States of America·R W HendrixG F Hatfull
Dec 21, 2000·Trends in Microbiology·R W HendrixS Casjens
Aug 24, 2001·Journal of Molecular Biology·A J ClarkT S Dhillon
Aug 10, 2002·Journal of Bacteriology·Jeffrey G LawrenceRoger W Hendrix
Apr 23, 2003·Cell·Marisa L PedullaGraham F Hatfull
Oct 24, 2003·Current Opinion in Microbiology·Roger W Hendrix
Mar 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Tony KwanJerry Pelletier
Sep 16, 2005·Nature·Curtis A Suttle
Sep 1, 1994·Applied and Environmental Microbiology·C A Suttle, A M Chan
Jan 24, 2006·Journal of Bacteriology·Tony KwanJerry Pelletier
Jun 23, 2006·PLoS Genetics·Graham F HatfullRoger W Hendrix
Dec 23, 2006·Science·David I HanauerGraham F Hatfull
May 8, 2007·Virology·Gipsi Lima-MendezRaphaël Leplae
Aug 28, 2007·Current Opinion in Microbiology·Elizabeth J SummerRy Young
Feb 1, 2008·Molecular Biology and Evolution·Gipsi Lima-MendezRaphaël Leplae
Jun 14, 2008·Research in Microbiology·Sherwood R Casjens
Oct 1, 2008·Current Opinion in Microbiology·Graham F Hatfull
Mar 17, 2009·Journal of Molecular Biology·Charles R StewartMarisa L Pedulla
Nov 26, 2009·Nucleic Acids Research·Raphaël LeplaeAriane Toussaint
Jan 13, 2010·Journal of Molecular Biology·Graham F HatfullRoger W Hendrix
Jun 10, 2010·Annual Review of Microbiology·Graham F Hatfull
Aug 20, 2010·BMC Bioinformatics·L Steven JohnsonElon Portugaly
Oct 30, 2010·Virology Journal·Vasiliy M PetrovJim D Karam

❮ Previous
Next ❯

Citations

Nov 29, 2013·Genome Announcements·Graham F HatfullUNKNOWN Phage Hunters Integrating Research and Education (PHIRE) Program
Feb 24, 2012·Journal of Virology·Catherine MageeneyGraham F Hatfull
Jul 20, 2013·BMC Genomics·Andrea I Moreno SwittMartin Wiedmann
Jul 23, 2013·PloS One·Welkin H PopeGraham F Hatfull
Mar 22, 2014·PLoS Pathogens·Graham F Hatfull
Feb 6, 2016·Genome Announcements·Dylan ChudoffDavid Dunbar
Apr 18, 2014·Journal of Basic Microbiology·Chris R GissendannerAnn M Findley
May 7, 2016·Bioinformatics·James G LamineSerita M Nelesen
Jun 15, 2012·The Journal of General Virology·Dann TurnerDarren Reynolds
Oct 23, 2012·Virology·Deborah Jacobs-SeraGraham F Hatfull
Jun 20, 2015·Genome Announcements·Welkin H PopeGraham F Hatfull
Jun 20, 2015·Genome Announcements·Welkin H PopeGraham F Hatfull
Mar 9, 2013·RNA Biology·Ana SenčiloRoger W Hendrix
Aug 3, 2013·Virology·Laura LorenzLouise Temple
Mar 6, 2015·PloS One·Steven G CresawnGraham F Hatfull
Jun 25, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Jul 2, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Jul 2, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Jul 9, 2016·Genome Announcements·Graham F HatfullUNKNOWN Phage Hunters Integrating Research and Education (PHIRE) Program
Jul 16, 2016·Genome Announcements·Samantha Foltz, Allison A Johnson
Oct 16, 2016·Bacteriophage·Casey StamereilersPhilippos K Tsourkas
May 6, 2016·Molecular Microbiology·Rebekah M DedrickGraham F Hatfull
Aug 16, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Aug 16, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Aug 16, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Aug 16, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Aug 16, 2016·Genome Announcements·Matthew T MontgomeryGraham F Hatfull
Aug 20, 2016·Genome Announcements·Welkin H PopeGraham F Hatfull
Oct 1, 2016·Genome Announcements·Ivan ErillUNKNOWN 2015 UMBC Phage Hunters
Oct 1, 2016·Genome Announcements·Monique L MillsShallee T Page

❮ Previous
Next ❯

Software Mentioned

BLASTN
MySQL
BLASTP
Python Remote Objects ( Pyro )
Phamerator Objects Pyro
CLUSTALW
bl2seq
Ubuntu
BLAST
RPS

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.