Phase 1, 2, and 3 Sequence Examples

As a sequence progresses from phase 1 to phase 2 to phase 3, the same accession number is used to reference that sequence. Many sequences do not go through this order; some sequences are submitted as phase 1 and then are updated to a phase 3 record, whereas others are submitted only in the final phase 3 form. At all times, only the most recent version of a record with a given accession number is retrieved by NCBI's Entrez or BLAST services. It is possible to retrieve older versions, when they exist, by using the gi (geninfo) number instead of the accession number.

Phase 1 and 2 records are retrievable from the HTG division of GenBank and are included in the htgs and month BLAST databases, whereas Phase 3 records are retrievable from the relevant organismal division (such as Primate or Invertebrate) and are included in the nr and month BLAST databases. When viewing an HTG GenBank record, the status of a sequence is clearly indicated: the description "Phase 1" or "Phase 2" is included in the definition line for those sequences, and the keywords "HTG; HTGS_PHASE1" (or 2) are included in the KEYWORDS field. Phase 3 sequences that have been submitted through the HTG submission process do not indicate Phase 3 in the definition line but do contain the keyword "HTG" in the KEYWORDS field and are located in the appropriate division. For example, human phase 3 sequences are moved into the PRI (primate) division, C. elegans and Drosophila phase 3 sequences are moved into the INV (invertebrate) division, and Arabidopsis phase 3 sequences are moved into the PLN (plant) GenBank division.

Records that lack gaps in their sequence may be at phase 2, because the quality scores for their sequences are too low to meet the finished standard. Once the coverage of the clone reaches finished quality, the record can be promoted to phase 3.

The links below will take you to a chromosome 17 sequence that was initially submitted through HTG as a phase 1 sequence, then updated to phase 2, then phase 3. The phase 1 and 2 versions of this sequence are no longer present in the HTG GenBank division, and the phase 3 record is now deposited in the GenBank primate (PRI) division. A BLAST search that identifies this accession number (AC000003) will use the phase 3 version of this sequence, which will only be found in the nr database.


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Last updated: 2017-11-20T22:51:52Z