Annotation

Due to the lack of Guineapig protein and cDNA resources, the majority of the gene models are based on Genewise alignments of proteins from mammals. Alignments made from Guineapig proteins had UTR added using Guineapig cDNAs. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.

Mammalian Genome Project

Cavia porcellus is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. A subset of these species are being sequenced in further depth. The aim is to increase our understanding of functional elements, especially in the human genome.