title: PolyPhred analysis software for mutation detection from fluorescence-based sequence data.
abstract: The ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect. The software is being continually updated to permit further automation of mutation analysis. Currently, however, at least some manual review is required if one wishes to identify 100% of the variants in a sample set.
authors.affiliation: Harvard Medical School - Partners Healthcare Center for Genetics and Genomics, Boston, Massachusetts, USA.
authors.forename: Kate T
authors.initials: KT
authors.lastname: Montgomery
authors.forename: Oleg
authors.initials: O
authors.lastname: Iartchouck
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Stephanie
authors.initials: S
authors.lastname: Loomis
authors.forename: Vanessa
authors.initials: V
authors.lastname: Obourn
authors.forename: Raju
authors.initials: R
authors.lastname: Kucherlapati
mesh_terms: D000465:Algorithms; D001331:Automation; D004247:DNA / Q000235:genetics; D004252:DNA Mutational Analysis / Q000706:statistics & numerical data*; D005456:Fluorescent Dyes; D014644:Genetic Variation; D005826:Genetics, Medical / Q000706:statistics & numerical data*; D015894:Genome, Human; D006801:Humans; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data; D012984:Software
chemical_list: D005456:Fluorescent Dyes; D004247:DNA