title: Sequence verification of synthetic DNA by assembly of sequencing reads.
abstract: Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Washington Street MC 0477, Blacksburg, VA 24061, USA.
authors.forename: Mandy L
authors.initials: ML
authors.lastname: Wilson
authors.forename: Yizhi
authors.initials: Y
authors.lastname: Cai
authors.forename: Regina
authors.initials: R
authors.lastname: Hanlon
authors.forename: Samantha
authors.initials: S
authors.lastname: Taylor
authors.forename: Bastien
authors.initials: B
authors.lastname: Chevreux
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.forename: Brett M
authors.initials: BM
authors.lastname: Tyler
authors.forename: Jean
authors.initials: J
authors.lastname: Peccoud
mesh_terms: D020451:Contig Mapping; D005813:Genes, Synthetic; D010957:Plasmids / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface