We strive for
in development of our methods. The following software is available:
Quantitative Enrichment of Sequence Tags: QuEST (updated 6/15/09)
QuEST works with ChIP-seq data. It finds sites in the genome that have enrichment signals, and are therefore candidates for transcription factor binding sites. QuEST is published (pdf).
Genomic Evolutionary Rate Profiling: GERP (updated 2/11/08)
GERP is a framework for constrained element identification that utilizes quantification of nucleotide substitution events within a multiple sequence alignment. GERP is published (pdf).
Multivariate Analysis of Protein Polymorphism: MAPP (updated 6/28/05)
MAPP quantifies physicochemical constraint violation of all possible amino acid substitutions, using a multiple alignment of protein sequences related by a phylogenetic tree. MAPP is published (pdf).
Application for Browsing Constraints: ABC (updated 6/28/05)
The ABC is Java software for the exploration of multiple sequence alignments and data typically associated with genomic alignments. The ABC is published (pdf).
Branch Manager: BM (updated 12/28/06)
The BM reads a phylogenetic tree with branch lengths and outputs a weight for each sequence that describes its contribution to the total information captured by the tree. BM is published (pdf). Download the zipped BM folder.
|Other possibly useful software|
Marker (zip of jar and documentation; updated 6/28/05)
A super-lightweight Java program for interactive scoring of medium-sized features in large image files, as illustrated by the excerpt from a large image on the right. Unpublished.
Partially funded by NIH/NHGRI