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.......................................................
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