Lastz/chain/net/multiz considerations/caveats/restrictions/limitations

Introduction

The lastz/chain/net/multiz processing pipeline is the primary alignment procedure used at the U.C. Santa Cruz Genomics Institute to produce multiple alignments. There are a number of considerations that should be taken into account by consumers of the resulting data that could certainly affect conclusions drawn from such analysis.

lastz

As with any alignment algorithm, the choice of parameters for lastz is critical to the results produced by this alignment program. Typically the parameters chosen fall into three categories based on the phylogenetic distance and/or clade relationship of target and query sequences.

1. primate to primate alignments (e.g. human<->chimp)
2. closer phylogenetic relationship (e.g. human<->mouse)
3. more distant phylgenetic relationship (e.g. human<->fish)