Table 1.
MatchMiner LookUp search options
| Identifier type | Input algorithm | Output algorithm |
| Name (Gene symbol, alias or descriptive name) | HUGO then Alias | HUGO then Alias |
| Starts with Official. If not found, proceeds through all other sources. | Returns the HUGO name. If no name is flagged as HUGO, returns all aliases. | |
| ALL (HUGO and Alias) | ALL (HUGO and Alias) | |
| Searches all data sources for all matches to the symbol and flags those that are HUGO. | Returns all gene symbols and flags the HUGO symbol. | |
| Official | Official | |
| Searches all data sources for match as the HUGO name. | Returns the HUGO name. If not found, nothing is returned. | |
| Long | Long | |
| Searches all data sources for descriptive name. | Returns all descriptive names. | |
| GenBank accession number | ALL | ALL |
| Searches all data sources starting with UCSC known genes, then LocusLink, UniGene and UCSC ESTs until match found. | Returns accession number from UCSC known genes. If not found, proceeds through UniGene then UCSC EST. | |
| Data-source specific | Data-source specific | |
| Look up input in a specific data source. | Returns accession numbers found in a particular data source. | |
| IMAGE clone | UniGene | UniGene |
| Only data source with IMAGE clone ids. | Returns all IMAGE clone IDs associated with the UniGene | |
| Cytogenetic location | ALL | ALL |
| Searches all gene indexes for matching chromosome band. | Returns chromosome band from UCSC sequence to band translation. If not found, proceeds through all other sources with multiple bands listed separately. | |
| UCSC | ||
| Returns chromosome band from UCSC sequence to band translation. | ||
| Database id | UniGene | UniGene |
| Searches gene index for matching UniGene id. | Returns UniGene id. | |
| Affymetrix | Affymetrix | |
| Searches gene index for matching Affymetrix probe set identifier. | Returns Affymetrix probe set identifier. | |
| Sequence location number (bp) | Not implemented | Transcription Start |
| Returns transcription start from UCSC Known Genes. If not found, proceeds to UCSC EST. | ||
| FISH clone | UCSC | UCSC |
| Searches UCSC FISH clones for match to gene index based on sequence position overlap with UCSC known genes. | Returns FISH clone id. |