A third approach to gene prediction suggests thousands of additional human transcribed regions.

ABSTRACT: The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome. Many algorithms for computational gene prediction have been described, ultimately derived from two basic concepts: (1) modeling gene structure and (2) recognizing sequence similarity. Successful hybrid methods combining these two concepts have also been developed. We present a third orthogonal approach to gene prediction, based on detecting the genomic signatures of transcription, accumulated over evolutionary time. We discuss four algorithms based on this third concept: Greens and CHOWDER, which quantify mutational strand biases caused by transcription-coupled DNA repair, and ROAST and PASTA, which are based on strand-specific selectio

SUBMITTER: Glusman G 

PROVIDER: S-EPMC1391917 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature