Biojava org biojava bio dist org biojava bio

Biojava • org. biojava. bio. dist org. biojava. bio. dp. onehead org. biojava. bio. dp. twohead org. biojava. bio. gui. sequence org. biojava. bio. program. blast 2 html 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. 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. 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. tools 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 Gene. DB, plus “dot plot” • Bio. Corba, Ace. DB 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