Bio Pat ML and DianaB The Bio Pat
Bio. Pat. ML and Diana-B The Bio. Pat. ML pattern description language and Diana-B, a genomic sequence browser. 30/01/2022 Stefan Maetschke
2 Queensland University of Technology (9) Contents l l l Bio. Pat. ML Software Diana-B Stefan Maetschke 30/01/2022
3 Queensland University of Technology (9) Bio. Pat. ML l l l Biological sequence pattern description language (DNA, RNA, AA) XML (e. Xtensible Markup Language) Unifies different pattern description paradigms Complex, hierarchical patterns Complete, annotated pattern description => simplifies: standardization of pattern descriptions, pattern reuse, pattern exchange, compilation of pattern databases <Motif name alphabet threshold sequence Stefan Maetschke = = "Pribnow-box" "DNA" "0. 7" "TATAAT" /> 30/01/2022
4 Queensland University of Technology (9) Patterns l l l <Anchor> <Any> <Gap> <Motif> <Regex> <Prosite> <PWM> <Block> <Repeat> <Series> <Profile> Stefan Maetschke anchors a pattern at a given sequence position matches any sequence of the specified length variable, (weighted) gap between patterns motif with mismatches regular expression in PROSITE syntax position weight matrix block of aligned sequences direct or inverted repeat of a pattern set of patterns ordered series of possibly gapped patterns gapped aggregation of (overlapping) patterns 30/01/2022
5 Queensland University of Technology (9) Example <Annotations> <Annotation name="Pattern"> Promoter </Annotation> <Annotation name="Date"> 02. 06. 2006 </Annotation> </Annotations> <Series mode="BEST" threshold="0. 0"> <Motif name="-35 element" alphabet="DNA" sequence="TTGACA" threshold="0. 7"/> <Gap min. Length="15" max. Length="21" impact="0. 2" > 0. 15 0. 16 0. 20 0. 16 0. 09 0. 12 0. 11 </Gap> <Motif name="-10 element" alphabet="DNA" sequence="TATAAT" threshold="0. 7"/> </Series> Stefan Maetschke 30/01/2022
6 Queensland University of Technology (9) Jacobi Java for computational biology Library for biological sequence analysis l l Karl Gustav Jacobi 1804 - 1851 German Mathematician Stefan Maetschke l Similar to Bio. Java, Bio. Perl, . . . but. . . Easier to use Smart indexing system Advanced pattern description (Bio. Pat. ML parser) Unit tested 30/01/2022
7 Queensland University of Technology (9) Software Jacobi Bio. Pat. ML Beagle Diana-Web Diana-B Stefan Maetschke 30/01/2022
8 Queensland University of Technology (9) Diana-B Genomic sequence browser for Bio. Pat. ML patterns Stefan Maetschke 30/01/2022
9 Queensland University of Technology (9) Thank you Questions ? l l Diana-Web: http: //eresearch. fit. qut. edu. au/Bio. Pat. ML/Diana/ Bio. Pat. ML Manual: http: //eresearch. fit. qut. edu. au/Bio. Pat. ML/Diana. App/Diana 101/Bio. Pat. MLManual. pdf Stefan Maetschke 30/01/2022
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