We note here that inaccuracies in the mouse reference assembly will distort detection of CNVs [16], but since this factor will be consistent across genome-wide studies we do not consider its impact further.
Genomic sequences of HFR stretches from each of the clusters were extracted from the mouse reference assembly MGSCv37-C57BL/6J of NCBI build 37.2 and subjected to motif search analysis using the MEME Suite of tools [ 45].
Although PCR-based approaches [ 9], forms of restriction mapping [ 10, 11] and optical mapping [ 12] can be used to bridge these gaps or connect orphan scaffolds, there are still currently 628 gaps and 44 orphan scaffolds in the latest mouse reference assembly (GRCm38/mm10), and 357 gaps and 65 orphan scaffolds in the latest iteration of the human assembly (GRCh37/hg19).
In addition, we present here a novel use of template-strand analysis to localize fragments and orient contigs, which has yielded a more refined mouse reference assembly with 20.8 Mb of contigs corrected (see Additional file 6: Table S1) and 2.7 Mb of orphan scaffolds localized to specific regions (Table 1).
Kim Pruitt described the Consensus Coding Sequence (CCDS) project, is a collaboration between multiple centers with a goal of producing a set of high-quality protein coding region annotations for the human and mouse reference genome assemblies (12).
Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies.
The Consensus Coding Sequence (CCDS) collaboration involves curators at multiple centers with a goal of producing a conservative set of high quality, protein-coding region annotations for the human and mouse reference genome assemblies.
Comparative sequence similarity search to human and mouse genome sequences revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes HSA4 and MMU5 of the human and mouse reference genome assemblies pointing to highly conserved genome regions in these species.
The following database versions were used in all analyses: Mouse UniGene build #136 (March 26 , 2004, mouse SAGEmap (April 3, 2004) corresponding to the mouse UniGene #136, LocusLink (April 3, 2004), mouse genome assembly NCBI build 32 (November 2003), mouse Reference Sequence collection (April 3, 2004) and Gene Ontology database (July, 2004).
