Algorithms for Sequence Analysis via Mutagenesis
Keith, Jonathan M., Adams, Peter, Bryant, Darryn, Cochran, Duncan A., Lala, Gita H., & Mitchelson, Keith R. (2004) Algorithms for Sequence Analysis via Mutagenesis. Bioinformatics, 20(15), pp. 2401-2410.
Motivation: Despite many successes of conventional DNA
sequencing methods, some DNAs remain difficult or
impossible to sequence. Unsequenceable regions occur in the
genomes of many biologically important organisms, including
the human genome. Such regions range in length from
tens to millions of bases, and may contain valuable information
such as the sequences of important genes. The authors
have recently developed a technique that renders a wide range
of problematic DNAs amenable to sequencing. The technique
is known as sequence analysis via mutagenesis (SAM). This
paper presents a number of algorithms for analysing and
interpreting data generated by this technique.
Results: The essential idea of SAM is to infer the target
sequence using the sequences of mutants derived from the
target. We describe three algorithms used in this process.
The first algorithm predicts the number of mutants that will
be required to infer the target sequence with a desired level
of accuracy. The second algorithm infers the target sequence
itself, using the mutant sequences. The third algorithm
assigns quality values to each inferred base. The algorithms
are illustrated using mutant sequences generated in the
Availability: Software will be made available upon request.
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|Item Type:||Journal Article|
|Additional Information:||For more information, please refer to the publisher's website (link above) or contact the author: firstname.lastname@example.org|
|Subjects:||Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)|
|Divisions:||Past > QUT Faculties & Divisions > Faculty of Science and Technology|
|Copyright Owner:||Copyright 2004 Oxford University Press.|
|Deposited On:||06 Jun 2007|
|Last Modified:||29 Feb 2012 23:29|
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