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

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 descr...

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Autores principales: Tu, Shin-Lin, Staheli, Jeannette P., McClay, Colum, McLeod, Kathleen, Rose, Timothy M., Upton, Chris
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265842/
https://www.ncbi.nlm.nih.gov/pubmed/30445717
http://dx.doi.org/10.3390/v10110637
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author Tu, Shin-Lin
Staheli, Jeannette P.
McClay, Colum
McLeod, Kathleen
Rose, Timothy M.
Upton, Chris
author_facet Tu, Shin-Lin
Staheli, Jeannette P.
McClay, Colum
McLeod, Kathleen
Rose, Timothy M.
Upton, Chris
author_sort Tu, Shin-Lin
collection PubMed
description 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.
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spelling pubmed-62658422018-12-07 Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes Tu, Shin-Lin Staheli, Jeannette P. McClay, Colum McLeod, Kathleen Rose, Timothy M. Upton, Chris Viruses Article 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. MDPI 2018-11-15 /pmc/articles/PMC6265842/ /pubmed/30445717 http://dx.doi.org/10.3390/v10110637 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tu, Shin-Lin
Staheli, Jeannette P.
McClay, Colum
McLeod, Kathleen
Rose, Timothy M.
Upton, Chris
Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title_full Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title_fullStr Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title_full_unstemmed Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title_short Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes
title_sort base-by-base version 3: new comparative tools for large virus genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265842/
https://www.ncbi.nlm.nih.gov/pubmed/30445717
http://dx.doi.org/10.3390/v10110637
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