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Table 1 A sample of annotations found in one or more of the UCSC, Ensembl and NCBI genome browsers.

From: Comparison of human (and other) genome browsers

Type

Annotations

Mapping and sequence

Chromosome bands; GC percent; CpG Islands; restriction enzyme recognition sites; BAC and fosmid clones; STS markers from genetic, RH maps; Mitelman breakpoints

Genes, transcription and expression

RefSeq mRNAs; VEGA genes; Ensembl genes; UniGene; pseudogenes; retroposed genes; Non-coding RNA genes; tRNAs; mRNAs and ESTs; computational gene predictions; GNF Atlas expression values; Affymetrix microarray probes; DNase1 hypersensitive sites

Variation and repeats

SNPs from dbSNP, HapMap projects haplotypes; recombination rates and hotspots; segmental duplications; repetitive sequences (RepeatMasker); tandem repeats

Cross-species

Evolutionarily conserved regions; syntenic mappings to many organisms including chimp, mouse, rat, chicken, cow, dog, opossum, fish

  1. Abbreviations: BAC, bacterial artificial chromosome; EST, expressed sequence tag; GNF, Genomics Institute of the Novartis Research Foundation; NCBI, National Center for Biotechnology Information; RH, Radiation hybrid; SNP, single nucleotide polymorphism; STS, sequence-tagged site; UCSC, University of California Santa Cruz; VEGA, Vertebrate Genome Annotation.
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Human Genomics

ISSN: 1479-7364