Conservation Track

Conservation Track Implementation Notes

1) Track Components: Tables

   multizNway
   multizNwaySummary
   multizNwayFrames
   phastConsNway

2) Track Components: Files

 * Display:
       /gbdb/<db>/multizNway/*.maf
       /gbdb/<db>/phastConsNway/*.wib

 * Downloads:
       goldenPath/<db>/multizNway/chr*.maf
       goldenPath/<db>/multizNway/upstream*.maf
       goldenPath/<db>/phastConsNway/*

3) Track Components: TrackDb

 * Required:
       type wigMaf
       wiggle

 * Optional:
       speciesOrder
       speciesGroups
       summary
       frames

4) Most Conserved Track

 * Table:
       phastConsNwayElements

 * Files:
       NONE

5) Track Construction: Overview

 1. Create single-coverage pairwise alignments (axtNet)
 2. Create multiple alignment
 3. Generate conservation scores and conserved elements
 4. Add gap annotation to multiple alignment
 5. Create multiple alignment summary
 6. Create frame tables for multiple alignment

6) Pairwise Alignments: Procedure

 1. Blastz Alignment (blastz, lavToPsl)
 2. Chaining (axtChain, chainMergeSort, chainAntiRepeat)
 3. Netting (chainNet, netFilter)
 4. Extraction of single-coverage alignments from the net (netToAxt)

 *  All automated by doBlastzChainNet.pl
  (Thanks, Angie!!)

7) Pairwise Alignments: Parameters

   Blastz scoring matrix
   Blastz gap penalties, misc
   Lineage-specific repeat abridging
   Chaining min score, linear gap

8) Multiple Alignment

 * Inputs:
       1. Single-coverage pairwise alignments
       2. Species tree

 * Aligner:
       multiz (with autoMZ driver) or
       TBA (Threaded Blockset Aligner)

9) Conservation Scoring with PhastCons

 * Inputs:
       Multiple alignment
       Species tree with branch lengths
        (optionally two trees)

 * Parameters:  rho, expected-len, target-coverage

 * Output:
       Per-base probability
       Conserved elements

10) Multiple Alignment Summary and Annotations

   Gap Annotation (mafAddIRows)
   Summary table (hgLoadMafSummary)
   Coding frames (getFrames, etc.)