Conservation Track
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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.)