1. Biojava org.biojava.bio org.biojava.bio.dist org.biojava.bio.dp org.biojava.bio.dp.onehead org.biojava.bio.dp.twohead org.biojava.bio.gui org.biojava.bio.gui.sequence org.biojava.bio.program org.biojava.bio.program.blast2html org.biojava.bio.program.das org.biojava.bio.program.gff org.biojava.bio.program.phred org.biojava.bio.program.sax org.biojava.bio.program.search org.biojava.bio.program.ssbind org.biojava.bio.program.xff org.biojava.bio.program.xml org.biojava.bio.proteomics org.biojava.bio.searchorg.biojava.bio org.biojava.bio.dist org.biojava.bio.dp org.biojava.bio.dp.onehead org.biojava.bio.dp.twohead org.biojava.bio.gui org.biojava.bio.gui.sequence org.biojava.bio.program org.biojava.bio.program.blast2html org.biojava.bio.program.das org.biojava.bio.program.gff org.biojava.bio.program.phred org.biojava.bio.program.sax org.biojava.bio.program.search org.biojava.bio.program.ssbind org.biojava.bio.program.xff org.biojava.bio.program.xml org.biojava.bio.proteomics org.biojava.bio.search org.biojava.bio.seq org.biojava.bio.seq.db org.biojava.bio.seq.db.biosql org.biojava.bio.seq.db.emblcd org.biojava.bio.seq.genomic org.biojava.bio.seq.homol org.biojava.bio.seq.impl org.biojava.bio.seq.io org.biojava.bio.seq.io.agave org.biojava.bio.seq.io.game org.biojava.bio.seq.projection org.biojava.bio.seq.ragbag org.biojava.bio.symbol org.biojava.stats.svm org.biojava.stats.svm.tools org.biojava.utils org.biojava.utils.cache org.biojava.utils.io org.biojava.utils.stax org.biojava.utils.xml

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