6.8 years ago by
Washington University School of Medicine, St. Louis, USA
De novo gene prediction and genome annotation based on conservation, GC content, HMMs, etc.
These kind of methods were hot when sequencing ESTs and full-length transcripts was prohibitively expensive. Now you can just sequence the transcriptome and let the data tell you what regions of the genome are being transcribed and what the exon/intron structures of those transcripts are (both canonical and minor isoforms).
As RNA-seq and related assembly methods improve, annotating a new genome will become increasingly routine and automated. A lot of genome and cDNA 'finishing' tasks have already been eliminated by these new types of data and related analysis pipelines.