It is important that users understand how to assess transcript annotations that they see in GENCODE. Some transcript models have a high level of support through the entirety of their structure, while other transcripts are poorly supported with one or two ESTs. A new method is being developed to differentiate this level of support. This method relies on mRNA and EST alignments supplied by UCSC and Ensembl. The mRNA and EST alignments are compared to the GENCODE transcripts, and the transcripts are scored according to how well the alignment matches over its full length (for more details, see the Supplemental Methods). Figure 8 shows support level statistics on a set broken down by annotation method for GENCODE 7. The annotations are partitioned into those produced only by the automated process, and those only from the manual method and the merged annotations, where both processes result in the same annotation. For the analyzed subset of GENCODE, 38% of the transcripts have good full-length support and an additional 39% have a lower level. The different distribution of support levels between the annotations
