title: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
abstract: We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.
authors.affiliation: Department of Molecular Biophysics, German Cancer Research Centre Heidelberg, 69120 Heidelberg, Germany. bastien@chevreux.org
authors.forename: Bastien
authors.initials: B
authors.lastname: Chevreux
authors.forename: Thomas
authors.initials: T
authors.lastname: Pfisterer
authors.forename: Bernd
authors.initials: B
authors.lastname: Drescher
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Driesel
authors.forename: Werner E G
authors.initials: WE
authors.lastname: Müller
authors.forename: Thomas
authors.initials: T
authors.lastname: Wetter
authors.forename: Sándor
authors.initials: S
authors.lastname: Suhai
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D020451:Contig Mapping / Q000379:methods; D004285:Dogs; D020224:Expressed Sequence Tags; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011161:Porifera / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software; D027843:Vitis / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D018749:RNA, Plant