Increasing consensus accuracy in DNA fragment assemblies by incorporating fluorescent trace representations.
We present a new method for determining the consensus sequence in DNA fragment assemblies. The new method, Trace-Evidence, directly incorporates aligned ABI trace information into consensus calculations via our previously described representation, Trace-Data Classifications. The new method extracts and sums evidence indicated by the representation to determine consensus calls. Using the Trace-Evidence method results in automatically produced consensus sequences that are more accurate and less ambiguous than those produced with standard majority-voting methods. Additionally, these improvements are achieved with less coverage than required by the standard methods-using Trace-Evidence and a coverage of only three, error rates are as low as those with a coverage of over ten sequences.
Allex
C F
CF
Computer Sciences Department, University of Wisconsin-Madison 53706, USA. allex@cs.wisc.edu
Baldwin
S F
SF
Shavlik
J W
JW
Blattner
F R
FR
D000465:Algorithms; D001483:Base Sequence; D003201:Computers; D016384:Consensus Sequence; D004247:DNA / Q000235:genetics*; D016208:Databases, Factual; D005456:Fluorescent Dyes; D005821:Genetic Techniques; D006801:Humans; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012689:Sequence Homology, Nucleic Acid; D012984:Software
D005456:Fluorescent Dyes; D004247:DNA