Mouse strains

Assembly and annotation

The Mouse Genomes Project is an ongoing effort to sequence the genomes of the common laboratory mouse strains, cataloguing all forms of molecular variation. They have produced de novo assemblies and strain-specific gene annotation for 16 laboratory and wild-derived strains (129S1/SvImJ, A/J, ARK/J, BALB/cJ, C3H/HeJ, C57BL/6NJ, CAST/EiJ, CBA/J, DBA/2J, FVB/NJ, LP/J, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, SPRET/EiJ, and WSB/EiJ) from a mixture of short- and long-range illumina libraries, optical maps, and third generation sequencing.

The strain-specific genome annotation was created by a combination of mapping over Gencode M8 mouse transcripts, strain-specific RNA-seq to refine mapped transcripts with Augustus, and Augustus CGP (comparative gene prediction) with strain-specific RNA-seq to annotate novel or private transcripts.

The assemblies and annotation were loaded into the Ensembl framework and additional analyses were run. These included: repeatmasking using Repeatmasker; ab initio gene predictions from Genscan; CpG island identification; prediction of transcription start sites using Eponine; tRNA predictions from tRNAscan; alignments of sequences from UniProt, UniGene and the ENA vertebrate RNA collection. Protein domains were annotated using InterProScan.