Weirick, T., John, D., Uchida, S. (2016). Resolving the problem of multiple accessions of the same transcript deposited across various public databases. Briefings in bioinformatics, bbv067. PMID: 26921280
Given GTF- or GFF-formatted text, this view will return UGAs (hashes) for the given sequence features and check for the existence of sequence features or similar features in other databases. A similar feature is defined as whose start and stop location are within ±25% of the corresponding features of the query sequence. It should be noted that this does not guarantee accuracy; rather, it is a heuristic way to allow return of queries in a reasonable amount of time.
Given an accession number from one of the database included in the UGAHash, this view will return UGAs mapping to the given accession
The following data sources and versions of data sources are included in the UGAHash web tool.
|Ensembl||60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84|
|LNCipedia||1.2, 2.1, 3.1|
|NCBI||103, 104, 105, 106, 107|
Various views in the UGAHash web tool can be downloaded as JSON or when possible TSV. When downloads are available, a button labeled "Download" will appear at the top left corner of the page.
An SQL dump of the data contained in UGAHash can be downloaded here.