Biojava

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.pro
  gram org.biojava.bio.program.blast2html
  org.biojava.bio.program.das org.biojava.bio.prog
  ram.gff org.biojava.bio.program.phred
  org.biojava.bio.program.sax org.biojava.bio.prog
  ram.search org.biojava.bio.program.ssbind
  org.biojava.bio.program.xff org.biojava.bio.prog
  ram.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.se
q.db.emblcd org.biojava.bio.seq.genomic
org.biojava.bio.seq.homol org.biojava.bio.seq.im
pl 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.symbo
l org.biojava.stats.svm org.biojava.stats.svm.to
ols org.biojava.utils org.biojava.utils.cache
org.biojava.utils.io org.biojava.utils.stax
org.biojava.utils.xml
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Basics

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

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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

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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

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Extras 2

• Probability distributions over Alphabets

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Summary

• Many developers are working on and contributing
  to Biojava, not just at Hinxton
• Its a standard, and the only one (?)
• Thus we would like to use it no wheel
  re-invention
• Some aspects we dont like but advantages
  outweigh disadvantages

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Summary 2

• Useful to us but
• Needs extending we could define those
  extensions
• We want Artemis to speak Biojava