Leveraging the Mouse Genome for Gene Prediction in Human: From Whole-Genome Shotgun Reads to a Global Synteny Map

• DOI: 10.1101/gr.830003
• Publication Date: 2003-01-15T18:22:25Z
• Authors: Paul Flicek; Evan Keibler; Ping Hu; Ian Korf; Michael R. Brent
• Keywords: Synteny; Gene prediction; Sequence assembly; Hybrid genome assembly; Gene Annotation; Comparative Genomics

The availability of draft sequences for both the mouse and human genomes makes it possible, first time, to annotate whole mammalian using comparative methods. TWINSCAN is a gene-prediction system that combines methods single-genome predictors like GENSCAN with information derived from genome comparison, thereby improving accuracy. Because uses genomic sequence only, less biased toward highly and/or ubiquitously expressed genes than GENEWISE, GENOMESCAN, other based on evidence transcripts. We show improves gene prediction in intermediate products various stages sequencing analysis genome, low-redundancy, whole-genome shotgun reads assembly synteny map. prior state art even when alignments only 1X coverage are available. Gene accuracy steadily through 3X, more slowly 3X 4X, relatively little thereafter. map greatly speed computations, however. Our annotation conservative, predicting 25,622 genes, appears be one best de novo annotations date.