Scribd Logo
Upload

Welcome to Scribd!

  • Bio Java

    Uploaded by

    Mitasha Bharadwaj Arora
    10 views7 pages
    biojava course presentaion

    Copyright

    © Attribution Non-Commercial (BY-NC)

    Available Formats

    PPT, PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    Report this Document
    biojava course presentaion

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    10 views7 pages

    Bio Java

    Uploaded by

    Mitasha Bharadwaj Arora
    biojava course presentaion

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPT, PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 7

    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 Its a standard, and the only one (?) Thus we would like to use it no wheel reinvention Some aspects we dont like but advantages outweigh disadvantages

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

    You might also like