Annotation Release 101 for the bottlenose dolphin (Tursiops truncatus) is out in RefSeq! This annotation was based on the NIST Tur_tru v1 assembly, which has a four-fold increase in contiguity from the assembly used in the previous annotation. Over four billion RNA-Seq reads from skin and blood tissue were used for gene prediction. As a result of these improvements, the percent of partially-represented protein-coding genes went down from 24% to 4%. Over 2500 genes that were fragmented in the previous assembly were merged into complete genes. A total of 24,026 genes were annotated, and 17,096 of them were protein-coding. A full report on the annotation can be found here.
In an earlier blog post, we discussed how sequence updates in GRCh38, the most recent version of the human reference genome, filled in a gap in human chromosome 17 near position 21,300K and expanded the region by 500K (500,000 base pairs). In this post, we will again consider this same region, but with an emphasis now on how GRCh38 also improved the gene annotation.
In late December 2013, the Genome Reference Consortium (GRC) released an updated version of the human reference genome assembly, GRCh38, and submitted these new sequences to GenBank. This is the first time in four years that a new major version of the human genome has become available to the genomics community.
Perhaps you’ve been working on data mapped to the previous assembly (GRCh37) that became available in March 2009, or maybe you are still using an even earlier version, such as NCBI36 from March 2006. Is there a way to reduce the amount of time and effort required to reanalyze your data in the context of the new assembly?
Yes! It’s NCBI’s Genome Remapping Service, or NCBI Remap for short.