The Use of Phylogenetic Profiles for Gene Predictions

Title: The Use of Phylogenetic Profiles for Gene Predictions

Volume: 3 Issue: 3

Author(s): David A. Liberles, Anna Thoren, Gunnar von Heijne and Arne Elofsson

Affiliation:

Keywords: phylogenetic profile, phylgenetic reconstruction, gene prediction

Abstract: Determining gene functions from genomic sequences is a central goal of bioinformatics. Most purely computational approaches to this problem are based on the detection of genes with similar sequences. With the completion of fully sequenced genomes alternative approaches have become feasible. One such method is that of phylogenetic profiles. In this method a gene is described by its phylogenetic profile, i.e. a string that encodes the presence or absence of a homologous gene in other genomes. This string is then used to search for other genes with similar profiles. In this paper we briefly review the field as well as present an analysis on the performance of the method. We also discuss variations on this theme including inverse phylogenetic profiles and non-exact profiles using phylogenetic trees. In conclusion this indicates that phylogenetic profiles might be useful for some, but not all functional annotations. Functional annotation of genomes remains an important problem in genomics when no close ho mologs exist.

Cite this article as:

Liberles A. David, Thoren Anna, Heijne von Gunnar and Elofsson Arne, The Use of Phylogenetic Profiles for Gene Predictions, Current Genomics 2002; 3 (3) . https://dx.doi.org/10.2174/1389202023350499