Xrate Pipeline

xrate comparative genome annotation pipeline

1. (MANUAL STEP) repeat detection, softmasking

• • (TODO) build Repeat Masker
  • (TODO) install Piler

1. (MANUAL STEP) gene prediction; ortholog assignment; anchoring; multiple alignment

• • (TODO) automate Mercator Tutorial (strictly, Mercator + PECAN)
    • (TODO) build SNAP, install WUBlast (as per tutorial)...
    • (TODO) investigate use of Exonerate in place of SNAP, WUBlast

1. (SEMI-AUTOMATED STEP) xrate model training

• • Mercator Perl

1. (AUTOMATED STEP) xrate sliding-window scan using Window Licker
2. (IN DEVELOPMENT) estimate false positive rate via genome transducer simulation
3. (AUTOMATED STEP) map scan back to genome; store in database

• • Mercator Perl again
  • (TODO) populate Bio Store or Chado Database
  • (MANUAL STEP) interface to Generic Genome Browser

1. (AUTOMATED STEP) fly-specific filters (Affy transfrags)

Documentation

• How To Run Pipeline
• xrate software

Related analysis

• RNA gene family analysis
  • Homology-based predictions (Infernal Software, Rfam Database)
  • Rate measurement (e.g. Fly Nc Rna)
• UTR regulatory elements (e.g. Fly Zipcodes)

-- Ian Holmes, Andrew Uzilov, Robert Bradley

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

1. 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

1. 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

1. 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