A major category of sequenced peptides derived from processing of extracellular matrix proteins (20.3%).
Array comparative genomic hybridization (aCGH) to detect copy number variants (CNVs) in mammalian genomes has led to a growing awareness of the potential importance of this category of sequence variation as a cause of phenotypic variation.
For this analysis, each category of sequence was assembled into a single file for each strain to generate an overall percentage of identity.
Type II AFPs are unlikely to belong to this category of sequence, however, as most ultraconserved elements are found in the genomes of many species, whereas the distribution of type II AFP genes is extremely limited.
For all of these benchmark sequence sets, except for the 14 plant genomes, we first calculated trees based on contiguous-word frequencies, and we identified the word length k that produces the best results for the respective category of sequence sets, i.e. the trees with the smallest RF distances to the respective reference trees.
As discussed in a recent review, alternating and periodic copolymers belong to the broad category of sequence-controlled macromolecules.
However, various rice genome annotation projects provide systematic_locus_IDs that will serve as placeholders for names of these genes until they can be elevated into the category of sequenced genes of known function, at which time they will be assigned a gene name and a gene symbol.
For each category of sequences, frequencies of the distinct isotype sequences are shown as stacks.
Each category of sequences was compared with previously published reference sequences on vaginal samples (Table 1).
Insertions and deletions (indels) are a promising category of molecular sequence information that is largely ignored in phylogenetic reconstruction.
However, genome surveys also revealed an unexpectedly large extent of other categories of sequence variants, including copy-number variants (CNV), inversions, translocations, and small to large sequence insertions and deletions [ 7].
