Supplementary Material for: Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution

During the past decade, we have experienced a revolution in the
biological sciences resulting from the flux of information generated by
genome-sequencing efforts. Our understanding of living organisms, the
metabolic processes they catalyze, the genetic systems encoding cellular
protein and stable RNA constituents, and the pathological conditions
caused by some of these organisms has greatly benefited from the
availability of complete genomic sequences and the establishment of
comprehensive databases. Many research institutes around the world are
now devoting their efforts largely to genome sequencing, data collection
and data analysis. In this review, we summarize tools that are in
routine use in our laboratory for characterizing transmembrane transport
systems. Applications of these tools to specific transporter families
are presented. Many of the computational approaches described should be
applicable to virtually all classes of proteins and RNA molecules.