SF-track, classification and monomer-by-monomer annotation of alpha satellite suprachromosomal families and pericentromeric monomer layers in T2T primate genome assemblies.
Annotation tables are shown at: How_to_read_AS_annotation
Based on the phylogenetic and genomic analysis of alpha satellites in hg38 genome assembly. Alpha satellite monomer class sequences were established as multiple sequence alignment HMM profiles and processed by HMMER to create a monomer-by-monomer annotation track for UCSC Genome Browser.
See details: Altemose et al., 2021, Supplementary Materials and Methods, Section I. Sequence content and organization of centromeric regions. Classification of alpha satellite monomers into suprachromosomal families.
Nicolas Altemose et al., Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178(2022). DOI: 10.1126/science.abl4178
Uralsky, L. I.; Shepelev, V. A.; Alexandrov, A. A.; Yurov, Y. B.; Rogaev, E. I.; Alexandrov, I. A. Classification and Monomer-by-Monomer Annotation Dataset of Suprachromosomal Family 1 Alpha Satellite Higher-Order Repeats in Hg38 Human Genome Assembly. Data Brief 2019, 24, 103708. doi: doi.org/10.1016/j.dib.2019.103708.
Shepelev, V. A.; Uralsky, L. I.; Alexandrov, A. A.; Yurov, Y. B.; Rogaev, E. I.; Alexandrov, I. A. Annotation of Suprachromosomal Families Reveals Uncommon Types of Alpha Satellite Organization in Pericentromeric Regions of Hg38 Human Genome Assembly. Genom Data 2015, 5, 139–146. doi: doi.org/10.1016/j.gdata.2015.05.035.
Shepelev, V. A.; Alexandrov, A. A.; Yurov, Y. B.; Alexandrov, I. A. The Evolutionary Origin of Man Can Be Traced in the Layers of Defunct Ancestral Alpha Satellites Flanking the Active Centromeres of Human Chromosomes. PLoS Genet. 2009, 5 (9), e1000641. doi: doi.org/10.1371/journal.pgen.1000641.
Contact Fedor Ryabov <fedorrik1@gmail.com>
Contact Ivan A. Alexandrov <ivanalx@hotmail.com>
Fedor Ryabov (HSE University, Moscow, Russia)
Lev I. Uralsky (1. Sirius University of Science and Technology, Sochi, Russia; 2. Vavilov Institute of General Genetics, Moscow, Russia)
Valery A. Shepelev (Institute of Molecular Genetics, Moscow, Russia (currently retired))
Ivan A. Alexandrov (Tel Aviv University, Israel)