Genome Sequence Analysis 2004:Computational Gene Finding

Joel H. Graber, Associate Staff Scientist, The Jackson Laboratory

Powerpoint slides
Example sequences (fasta format)
Human p53 Genbank Record (the answer!)	D. melanogaster genomic sequence Genbank Record (positions 24000-54000) (sort of an answer)	D. rerio high throughput genome sequence (HTGS)
Links from the presentation
Eukaryotic gene predictions Genscan (ab initio), GenomeScan (hybrid) Twinscan (hybrid) FGENESH (ab initio) GeneMark.hmm (ab initio) MZEF (ab initio) GrailEXP (hybrid) GeneID (hybrid)	Prokaryotic Gene Prediction Glimmer GeneMark Critica ORNL Annotation Pipeline	Non-coding transcript tools and info tRNA tRNA-ScanSE FAStRNA snoRNA snoRNA database microRNA Sfold SIRNA
Papers of interest
Curr Opin Struct Biol. 2004 Jun;14(3):264-72. Recent advances in gene structure prediction.Brent MR, Guigo R. Brief Bioinform. 2000 Nov;1(4):381-8. Genome sequence comparisons: hurdles in the fast lane to functional genomics.Wiehe T, Guigo R, Miller W. Genome Res.2000 Oct;10(10):1631-42. An assessment of gene prediction accuracy in large DNA sequences. Guigo R, Agarwal P, Abril JF, Burset M, Fickett JW. Genome Res.2004 Jan;14(1):142-8. Computational gene prediction using multiple sources of evidence. Allen JE, Pertea M, Salzberg SL.