In addition to the targeted nuclear loci, reference-guided assembly of the off-target reads yielded complete or nearly complete plastome and nrDNA cistron sequences (Table 2).
Standard nomenclature was used for describing variants (www.hgvs.org), and the locus reference genomic sequence LRG_274 for LDLR was used.
CNV: copy number variation; EBI: European Bioinformatics Institute; GEN2PHEN: Genotype-To-Phenotype Databases Project; HGVS Human Genome Variation Society LOVDVD: Leiden Open Variation Database; LRG: Locus Reference Genomic; LSDB: Locus-specific Database; NCBI: National Center for Biotechnology Information.
Reference sequences for the MLH1, MSH2 and MSH6 genes were NM_000249.3, NM_000251.1 and NM_000179.2, respectively, as mentioned in the Locus Reference Genomic database.
These LRG (Locus Reference Genomic) sequences can be used as a framework for data exchange of annotated disease variants currently stored in diagnostic laboratories and LSDBs (Locus-Specific Databases).
There are also projects at European Bioinformatics Institute (EBI) and National Center for Biotechnology Information (NCBI) to develop reference sequences, locus reference genomics (LRGs) (http://www.lrg-sequence.org) and RefSeqGenes (http://www.ncbi.nlm.nih.gov/projects/RefSeq/RSG/), respectively.
The reference sequence should be complete and derived from either the NCBI RefSeq database (http://www.ncbi.nlm.nih.gov/RefSeq/) with the version number or the Locus Reference Genomic (LRG) database (http://www.lrg-sequence.org).org
Currently, the approved Recommended Systems include Mutalyzer for generating systematic HGVS names for variations (1), Locus Reference Genomic (LRG) sequence format for reference sequences (2), LOVD data management system for LSDBs (3), and HGVS Nomenclature (4).
STAR locus reference sets were also produced for S. epidermidis and S. haemolyticus, and BLASTN alignments were carried out between these reference sets and all of the other species genomes to confirm the cross species results.
Gene ontology (GO) terms were assigned to each of the overall heat responsive genes and a GO term enrichment analysis was carried out [ 29] using the Zea mays ssp maize genome locus reference (maizesequence.org).org
