Briefings in Bioinformatics Advance Access originally published online on February 3, 2006
Briefings in Bioinformatics 2006 7(1):113-115; doi:10.1093/bib/bbk008
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org
Pairwise sequence alignment—it's all about us!
Lisa Mullan, EMBL-European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. E-mail: lisa@ebi.ac.uk
| The first 10% of the full text of this article appears below. |
Pairwise alignment is one of the most fundamental tools of bioinformatics and underpins a variety of other, more sophisticated methods of annotation. Pairwise alignment in its most rigorous form uses a method called ‘dynamic programming’, which is highly accurate, but also incredibly costly to compute.
In order to align anything other than an exact alphabetic match, the algorithm has to know what it is looking for and how it can evaluate the worth of what it finds. To this end, ‘comparison matrices’ have been created which define a score for every possible match possibility—an effective tally of how well the computational alignment is doing. The software will search for the highest score available. The final score is relevant only with its resulting alignment and cannot be used outside this context.
In the case of DNA, comparison values