title: HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants.
abstract: Compaction of DNA into chromatin is a characteristic feature of eukaryotic organisms. The core (H2A, H2B, H3, H4) and linker (H1) histone proteins are responsible for this compaction through the formation of nucleosomes and higher order chromatin aggregates. Moreover, histones are intricately involved in chromatin functioning and provide a means for genome dynamic regulation through specific histone variants and histone post-translational modifications. 'HistoneDB 2.0--with variants' is a comprehensive database of histone protein sequences, classified by histone types and variants. All entries in the database are supplemented by rich sequence and structural annotations with many interactive tools to explore and compare sequences of different variants from various organisms. The core of the database is a manually curated set of histone sequences grouped into 30 different variant subsets with variant-specific annotations. The curated set is supplemented by an automatically extracted set of histone sequences from the non-redundant protein database using algorithms trained on the curated set. The interactive web site supports various searching strategies in both datasets: browsing of phylogenetic trees; on-demand generation of multiple sequence alignments with feature annotations; classification of histone-like sequences and browsing of the taxonomic diversity for every histone variant. HistoneDB 2.0 is a resource for the interactive comparative analysis of histone protein sequences and their implications for chromatin function. Database URL: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Eli J
authors.initials: EJ
authors.lastname: Draizen
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Alexey K
authors.initials: AK
authors.lastname: Shaytan
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.
authors.forename: Leonardo
authors.initials: L
authors.lastname: Mariño-Ramírez
authors.affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Talbert
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA panch@ncbi.nlm.nih.gov landsman@ncbi.nlm.nih.gov.
authors.forename: David
authors.initials: D
authors.lastname: Landsman
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA panch@ncbi.nlm.nih.gov landsman@ncbi.nlm.nih.gov.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D057225:Data Mining; D030562:Databases, Protein; D014644:Genetic Variation; D006657:Histones / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000737:chemistry; D016415:Sequence Alignment
chemical_list: D006657:Histones; D009707:Nucleosomes