Table 1 MatchMiner LookUp search options
From: MatchMiner: a tool for batch navigation among gene and gene product identifiers
Identifier type | Input algorithm | Output algorithm |
|---|---|---|
Name (Gene symbol, alias or descriptive name) | HUGO then Alias | HUGO then Alias |
| Â | 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. |
| Â | ALL (HUGO and Alias) | ALL (HUGO and Alias) |
| Â | 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. |
| Â | Official | Official |
| Â | Searches all data sources for match as the HUGO name. | Returns the HUGO name. If not found, nothing is returned. |
| Â | Long | Long |
| Â | Searches all data sources for descriptive name. | Returns all descriptive names. |
GenBank accession number | ALL | ALL |
| Â | 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. |
| Â | Data-source specific | Data-source specific |
| Â | Look up input in a specific data source. | Returns accession numbers found in a particular data source. |
IMAGE clone | UniGene | UniGene |
| Â | Only data source with IMAGE clone ids. | Returns all IMAGE clone IDs associated with the UniGene |
Cytogenetic location | ALL | ALL |
| Â | 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. |
| Â | Â | UCSC |
| Â | Â | Returns chromosome band from UCSC sequence to band translation. |
Database id | UniGene | UniGene |
| Â | Searches gene index for matching UniGene id. | Returns UniGene id. |
| Â | Affymetrix | Affymetrix |
| Â | Searches gene index for matching Affymetrix probe set identifier. | Returns Affymetrix probe set identifier. |
Sequence location number (bp) | Not implemented | Transcription Start |
| Â | Â | Returns transcription start from UCSC Known Genes. If not found, proceeds to UCSC EST. |
FISH clone | UCSC | UCSC |
| Â | Searches UCSC FISH clones for match to gene index based on sequence position overlap with UCSC known genes. | Returns FISH clone id. |