Any locus may be represented 0, 1 or >1 time, but entire chromosomes are only represented 0 or 1 times.Ī genome assembly for which a chromosome assembly is available for both sets of an individual's chromosomes. The collection of chromosome assemblies, unlocalized and unplaced sequences and alternate loci that represent an organism's genome. Any locus may be represented 0 or 1 time, and entire chromosomes are only represented 0 or 1 times. The collection of chromosome assemblies, unlocalized and unplaced sequences that represent an organism's genome. Assemblies are constructed from 1 or more assembly units. The set of chromosomes, unlocalized and unplaced (sometimes called 'random') and alternate sequences used to represent an organism's genome. Terms used in this model are defined below and a graphical representation is shown in figure 2. To accommodate this increased complexity, we have developed a more robust data model. For example, the current public human reference assembly ( GRCh38) has 8 different paths through the MHC region, a region known to have a high degree of allelic complexity. If a genome contains regions with complex allelic diversity, it may be necessary to produce more than 1 sequence path to fully represent that region. Large-scale structural variations, often in the form of Copy Number Variation (CNVs) are more prevalent than originally thought (see dbVar for more information). Subsequent genome analysis has shown that this model will not work for some parts of the genome. It was thought that the predominant form of variation was single nucleotide polymorphism ( SNP) and these polymorphisms would be represented as annotation on the chromosome sequence. That is, a single set of overlapping sequences could be selected to produce a non-redundant chromosome sequence (with gaps) that would fully represent the sequence at all loci. When genome sequencing initially started it was thought that the genome assembly could be represented by a single 'Golden Path'. Developing a robust assembly model allows us to tie together the output of assembly algorithms with the biological model that has developed over years of genomic research. Typically, not all sequences can be can be ordered and oriented. In fact, the output of most assembly algorithms is a set of contigs and scaffolds that are then ordered and oriented using external data (such as mapping information). Because of the complexities found in many organisms, it is currently not possible to obtain a complete chromosome sequence. These sequences are then assembled to try to recreate the chromosome sequences (see Assembly Basics for more information). To accomplish genome sequencing, the genome is fragmented and small pieces are sequenced many times. However, current sequencing technology does not allow for the complete sequencing of a single chromosome. However, most representations of an organism's genome tend to only represent the haploid state, as shown in figure 1. While many eukaryotes tend to exist in a diploid state (2 copies of each autosome and 2 sex chromosomes) other organisms, such as plants, can have many copies (e.g. While bacteria can have a single chromosome, often accompanied by extra-chromosomal plasmids, eukaryotes often have multiple chromosomes, with each chromosome being represented greater than 1 time. The genome of an organism consists of a set of chromosomes. 1: An ideogram representation of the human genome.
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