Random Projects2006

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Random Projects2006

Holmes lab targets/projects for 2006.

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Fruitfly RNA analysis

(See Fruitfly Bioinformatics Resources)

  • High-quality set of multi-fruitfly gene annotations
  • Multiple alignments of all fruitfly ncRNA genes
    • miRNA
    • rRNA
    • other RNA
  • Investigate changes in structure

Noncoding RNA algorithms

(See Multiple RNAAlignment, Xgram Software)

  • Develop a QRNA-like xgram model with protein, ncRNA, fast-null, slow-null, intermediate-null (etc) models
  • Benchmark existing methods
    • stemloc
    • xgram
  • Improve specificity
    • stemloc: phylogenetic multiple alignment
    • stemloc: alignment envelope from multiple alignment
  • Improve RNA multiple alignment
    • stemloc: lexicalised grammar for stacking (Ticket:141)
  • Investigate variation of evolutionary rates in basepairs/stems

Transposons

(See Transposon Papers)

  • Use stochastic tree-adjoining grammars (or context-sensitive HMMs?) to annotate LTRs
  • Develop general algorithms for transposon annotation
    • See prior work of Eddy and Bao; Myers and Edgar; Caspi and Pachter; Bejerano et al
  • Apply algorithms to ongoing genome projects
  • Quantitative prediction of Tc1/mariner activity? (protein-DNA binding, etc.)
    • Models of transposon population dynamics, ecology

xgram paper

(See Xgram Software, Xgram Format)

Handel

(See Handel Package)

  • Long indels in handalign
    • Finish transducer code
  • Publish!
  • Rasmus Nielsen collaboration

Generic Genome Browser

  • Initial release
  • Publication

Microbial genomics

  • Acidothermus cellulolyticus annotation

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