uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Is Sequence Alignment an Art or a Science?
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
2015 (English)In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 40, no 1, 14-26 p.Article in journal (Refereed) Published
Abstract [en]

Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative sequence analyses in evolutionary biology. These alignments are often recognized as representing the homology relations of the aligned nucleotides, but this is a necessary requirement only for phylogenetic analyses. Unfortunately, existing computer programs for sequence alignment are not based explicitly on detecting the homology of nucleotides, and so there is a notable gap in the existing bioinformatics repertoire. If homology is the goal, then current alignment procedures may be more art than science. To resolve this issue, I present a simple conceptual scheme relating the traditional criteria for homology to the features of nucleotide sequences. These relations can then be used as optimization criteria for nucleotide sequence alignments. I point out the way in which current computer programs for multiple sequence alignment relate to these criteria, noting that each of them usually implements only one criterion. This explains the apparent dissatisfaction with computerized sequence alignment in phylogenetics, as any program that truly tried to produce alignments based on homology would need to simultaneously optimize all of the criteria.

Place, publisher, year, edition, pages
2015. Vol. 40, no 1, 14-26 p.
Keyword [en]
Multiple alignment, alignment algorithm, sequence homology
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-249025DOI: 10.1600/036364415X686305ISI: 000350250100003OAI: oai:DiVA.org:uu-249025DiVA: diva2:807777
Available from: 2015-04-24 Created: 2015-04-10 Last updated: 2015-04-24Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Morrison, David A.
By organisation
Systematic Biology
In the same journal
Systematic Botany
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 226 hits
ReferencesLink to record
Permanent link

Direct link