Genome assembly search and request

 - Advanced search help ⓘ

All searches are case-insensitive. Single-word searches default to prefix matching if an exact match is not found.

  • Force inclusion: Use a + sign before +word to ensure it appears in result.
  • Exclude words: Use a - sign before -word to exclude it from the search result.
  • Wildcard search: Add an * (asterisk) at end of word* to search for all terms starting with that prefix.
  • Phrase search: Enclose "words in quotes" to search for the exact phrase.
Assembly View/Request ⓘ
  1. In available browsers - the assembly exists in the UCSC browser system, the view link will lead to the browser
  2. Can be requested - assembly is not yet in the UCSC browser system, the request link will open a request form to ask for the assembly to be added to the UCSC browser system
Assembly status ⓘ
  1. Latest - the most recent of all the versions for this assembly chain
  2. Replaced - this version has been replaced by a newer version of the assembly in the same chain
  3. Suppressed - this version of the assembly has been suppressed
  4. An assembly chain is the collection of all versions for the same assembly accession.
RefSeq category ⓘ
  1. Reference genome - a manually selected high quality genome assembly that NCBI and the community have identified as being important as a standard against which other data are compared
  2. Representative genome - a genome computationally or manually selected as a representative from among the best genomes available for a species or clade that does not have a designated reference genome
  3. There are assemblies which have no RefSeq category assignment
  4. For more information, see also: www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/#referencegenome
Assembly level ⓘ
  1. Complete genome - all chromosomes are gapless and have no runs of 10 or more ambiguous bases (Ns), there are no unplaced or unlocalized scaffolds, and all the expected chromosomes are present (i.e. the assembly is not noted as having partial genome representation). Plasmids and organelles may or may not be included in the assembly but if present then the sequences are gapless.
  2. Chromosome - there is sequence for one or more chromosomes. This could be a completely sequenced chromosome without gaps or a chromosome containing scaffolds or contigs with gaps between them. There may also be unplaced or unlocalized scaffolds.
  3. Scaffold- some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized.
  4. Contig- nothing is assembled beyond the level of sequence contigs
Word match control ⓘFor multiple word search, May match will allow any combination of word matches, where Must match will force all words to be in the search result.
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