Flexible mapping of homology onto structure with Homolmapper

Background: Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine. Results: We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself) and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits fac...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Nathan C. Rockwell, J. Clark Lagarias
• Keywords: BMCBI 2007, Homology Relationships, Protein Sequences, Proteins