Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2018 Nov 18

PMID 30445717

Citations 13

Authors

Shin-Lin Tu

Jeannette P Staheli

Colum McClay

Kathleen McLeod

Timothy M Rose

Chris Upton

Affiliations

Soon will be listed here.

Abstract

Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves can contain gene annotations. This report describes new features added to Base-By-Base over the last 7 years. The two most significant additions are: (1) The recoding and inclusion of "consensus-degenerate hybrid oligonucleotide primers" (CODEHOP), a popular tool for the design of degenerate primers from a multiple sequence alignment of proteins; and (2) the ability to perform fuzzy searches within the columns of sequence data in multiple sequence alignments to determine the distribution of sequence variants among the sequences. The intuitive interface focuses on the presentation of results in easily understood visualizations and providing the ability to annotate the sequences in a multiple alignment with analytic and user data.

Citing Articles

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References

Brodie R, Roper R, Upton C . JDotter: a Java interface to multiple dotplots generated by dotter. Bioinformatics. 2004; 20(2):279-81. DOI: 10.1093/bioinformatics/btg406. View

Waterhouse A, Procter J, Martin D, Clamp M, Barton G . Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009; 25(9):1189-91. PMC: 2672624. DOI: 10.1093/bioinformatics/btp033. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Chouhy D, Kocjan B, Staheli J, Bolatti E, Hosnjak L, Sagadin M . Detection of novel Betapapillomaviruses and Gammapapillomaviruses in eyebrow hair follicles using a single-tube 'hanging droplet' PCR assay with modified pan-PV CODEHOP primers. J Gen Virol. 2017; 99(1):109-118. PMC: 6537621. DOI: 10.1099/jgv.0.000988. View

Wilson C, Wong S, Muller J, Davidson C, Rose T, Burd P . Type C retrovirus released from porcine primary peripheral blood mononuclear cells infects human cells. J Virol. 1998; 72(4):3082-7. PMC: 109758. DOI: 10.1128/JVI.72.4.3082-3087.1998. View

Rose T . CODEHOP-mediated PCR - a powerful technique for the identification and characterization of viral genomes. Virol J. 2005; 2:20. PMC: 1079958. DOI: 10.1186/1743-422X-2-20. View

Hillary W, Lin S, Upton C . Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments. Microb Inform Exp. 2012; 1(1):2. PMC: 3348662. DOI: 10.1186/2042-5783-1-2. View

Philipp-Staheli J, Marquardt T, Thouless M, Bruce A, Grant R, Tsai C . Genetic variability of the envelope gene of Type D simian retrovirus-2 (SRV-2) subtypes associated with SAIDS-related retroperitoneal fibromatosis in different macaque species. Virol J. 2006; 3:11. PMC: 1450265. DOI: 10.1186/1743-422X-3-11. View

Edgar R . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMC: 390337. DOI: 10.1093/nar/gkh340. View

10.

Sievers F, Higgins D . Clustal Omega, accurate alignment of very large numbers of sequences. Methods Mol Biol. 2013; 1079:105-16. DOI: 10.1007/978-1-62703-646-7_6. View

11.

Katoh K, Frith M . Adding unaligned sequences into an existing alignment using MAFFT and LAST. Bioinformatics. 2012; 28(23):3144-6. PMC: 3516148. DOI: 10.1093/bioinformatics/bts578. View

12.

Pervez M, Babar M, Nadeem A, Aslam N, Naveed N, Ahmad S . IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments. Evol Bioinform Online. 2015; 11:35-42. PMC: 4362671. DOI: 10.4137/EBO.S18980. View

13.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

14.

Rose T, Schultz E, Henikoff J, Pietrokovski S, McCALLUM C, Henikoff S . Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 1998; 26(7):1628-35. PMC: 147464. DOI: 10.1093/nar/26.7.1628. View

15.

Altschul S, Gish W, Miller W, Myers E, Lipman D . Basic local alignment search tool. J Mol Biol. 1990; 215(3):403-10. DOI: 10.1016/S0022-2836(05)80360-2. View

16.

Nix W, Oberste M, Pallansch M . Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol. 2006; 44(8):2698-704. PMC: 1594621. DOI: 10.1128/JCM.00542-06. View

17.

Brodie R, Smith A, Roper R, Tcherepanov V, Upton C . Base-By-Base: single nucleotide-level analysis of whole viral genome alignments. BMC Bioinformatics. 2004; 5:96. PMC: 481056. DOI: 10.1186/1471-2105-5-96. View

18.

Larsson A . AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014; 30(22):3276-8. PMC: 4221126. DOI: 10.1093/bioinformatics/btu531. View

19.

Boyce R, Chilana P, Rose T . iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Res. 2009; 37(Web Server issue):W222-8. PMC: 2703993. DOI: 10.1093/nar/gkp379. View

20.

Borsting C, Hummel R, Schultz E, Rose T, Pedersen M, Knudsen J . Saccharomyces carlsbergensis contains two functional genes encoding the acyl-CoA binding protein, one similar to the ACB1 gene from S. cerevisiae and one identical to the ACB1 gene from S. monacensis. Yeast. 1998; 13(15):1409-21. DOI: 10.1002/(SICI)1097-0061(199712)13:15<1409::AID-YEA188>3.0.CO;2-A. View