Bioperl course-Catherine Letondal and Katja Schuerer.PDF

TableofContents 1.Generalintroduction........................................................................1 1.1.Bioperldocumentation...............................................................1 1.2.Generalbioperlclasses...............................................................1 2.Sequences.................................................................................3 2.1.TheBio::SeqIOclass.............................................................3 2.1.1.FormatConverter.............................................................3 2.2.Sequenceclasses....................................................................4 2.2.1.Introduction..................................................................4 2.2.2.Buildingmechanismssummary................................................5 2.2.3.AdeeperinsightintotheBio::Seqclass.........................................6 2.2.4.Bioperl’Sequence’classesstructure...........................................12 2.3.FeaturesandLocationclasses........................................................13 2.3.1.Feature.....................................................................13 2.3.2.Codereading:extractingCDS................................................16 2.3.3.Tagsystem.................................................................17 2.3.4.Location....................................................................18 2.3.5.Graphicalviewoffeatures....................................................20 2.4.Sequenceanalysistools.............................................................21 3.Alignments...............................................................................25 3.1.AlignIO...........................................................................25 3.2.SimpleAlign.......................................................................26 3.3.Codereading:protal2dna............................................................30 4.Analysis.......................................................