xrate comparative genome annotation pipeline

A work in progress...

1. (MANUAL STEP) repeat detection, softmasking
   • (TODO) build RepeatMasker
   • (TODO) install Piler
2. (MANUAL STEP) gene prediction; ortholog assignment; anchoring; multiple alignment
   • (TODO) automate MercatorTutorial (strictly, Mercator + PECAN)
     • (TODO) build SNAP, install WUBlast (as per tutorial)...
     • (TODO) investigate use of Exonerate in place of SNAP, WUBlast
3. (SEMI-AUTOMATED STEP) xrate model training
   • MercatorPerl
4. (AUTOMATED STEP) xrate sliding-window scan using WindowLicker
5. (IN DEVELOPMENT) estimate false positive rate via genome transducer simulation
6. (AUTOMATED STEP) map scan back to genome; store in database
   • MercatorPerl again
   • (TODO) populate BioStore or ChadoDatabase
   • (MANUAL STEP) interface to GenericGenomeBrowser
7. (AUTOMATED STEP) fly-specific filters (Affy transfrags)

Documentation

• HowToRunPipeline
• xrate software

Related analysis

• RNA gene family analysis
  • Homology-based predictions (InfernalSoftware, RfamDatabase)
  • Rate measurement (e.g. FlyNcRna)
• UTR regulatory elements (e.g. FlyZipcodes)

-- IanHolmes, AndrewUzilov, RobertBradley

Meeting notes

agenda 10/18/2007

preliminary outline (+timeline?) of the Drosophila screen paper

1. experimental followup:
   • PCR/sequencing/etc experiments; imminent visit to Sue Celniker
   • targeted expression: Eric Lai, Pavel Tomancak
   • modENCODE
2. informatics followup:
   • 100/300 prediction set: GFF, FASTA, Stockholm; put into GBrowse
   • broad-trend GO analysis of gene-overlapping hits
   • stemloc alignment/clustering of hit regions
   • Avinash's simulator & false positive estimates
3. estimate write/submit/publish schedule for Drosophila screen
   • misc analysis Q's: tetra/triloops? RNA-derived repeats? phylogenetic distribution? population variation? Drosophila vs Anopheles, Bombyx?

ideas for future runs of the pipeline

1. desired enhancements:
   • grammars & modeling
   • pipeline & infrastructure
   • browser
2. applications to other species clades:
   • fungal genomes
   • nematodes
   • mammals/vertebrates/eutheria

meeting with Sue & Joe, 10/18/2007

• enrich for longer hits, separate out putative short miRNAs
• post pipeline results on wiki