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Biojava

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Biojava org.biojava.bio org.biojava.bio.dist org.biojava.bio.dp org.biojava.bio.dp.onehead ... org.biojava.utils.io org.biojava.utils.stax org.biojava.utils.xml – PowerPoint PPT presentation

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Title: 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
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
  • 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

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