Download Biojava

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.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
Basics
• Sequence has features
• Feature has annotation + other Features +
Location
• Location can have a range of locations so
2100..2500 [2100..2200, 2300..2500]
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
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
Extras 2
• Probability distributions over Alphabets
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 reinvention
• Some aspects we don’t like but advantages
outweigh disadvantages
Summary 2
• Useful to us but;
• Needs extending – we could define those
extensions
• We want Artemis to speak Biojava