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Biojava

Biojava.

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Biojava

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  1. Biojava org.biojava.bio.seqorg.biojava.bio.seq.dborg.biojava.bio.seq.db.biosqlorg.biojava.bio.seq.db.emblcdorg.biojava.bio.seq.genomicorg.biojava.bio.seq.homolorg.biojava.bio.seq.implorg.biojava.bio.seq.ioorg.biojava.bio.seq.io.agaveorg.biojava.bio.seq.io.gameorg.biojava.bio.seq.projectionorg.biojava.bio.seq.ragbagorg.biojava.bio.symbolorg.biojava.stats.svmorg.biojava.stats.svm.toolsorg.biojava.utilsorg.biojava.utils.cacheorg.biojava.utils.ioorg.biojava.utils.staxorg.biojava.utils.xml • org.biojava.bioorg.biojava.bio.distorg.biojava.bio.dporg.biojava.bio.dp.oneheadorg.biojava.bio.dp.twoheadorg.biojava.bio.guiorg.biojava.bio.gui.sequenceorg.biojava.bio.programorg.biojava.bio.program.blast2htmlorg.biojava.bio.program.dasorg.biojava.bio.program.gfforg.biojava.bio.program.phredorg.biojava.bio.program.saxorg.biojava.bio.program.searchorg.biojava.bio.program.ssbindorg.biojava.bio.program.xfforg.biojava.bio.program.xmlorg.biojava.bio.proteomicsorg.biojava.bio.search

  2. Basics • Sequence has features • Feature has annotation + other Features + Location • Location can have a range of locations so 2100..2500 [2100..2200, 2300..2500]

  3. Tools • Lots of methods available to manipulate these objects such as reverse complement, translation, iterators • Parsers built in to input/output sequence/features etc: EMBL, GFF, Blast, meme, XML (SAX), GAME, AGAVE, XFF 0.2 proposal, Phred + etc, etc • Visualisation: Artemis/Apollo style interfaces – also static image maps on GeneDB, plus “dot plot” • BioCorba, AceDB client

  4. Extras • Caching system built in, you define the behaviour • Utilities for analysing protein sequences: digest, masscalc • Distributed Annotation System DAS – work in progress but read only clients available • HMM and Dynamic Programming Algorithms

  5. Extras 2 • Probability distributions over Alphabets

  6. Summary • Many developers are working on and contributing to Biojava, not just at Hinxton • It’s a standard, and the only one (?) • Thus we would like to use it – no wheel re-invention • Some aspects we don’t like but advantages outweigh disadvantages

  7. Summary 2 • Useful to us but; • Needs extending – we could define those extensions • We want Artemis to speak Biojava

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