Sequence database setup
Mascot Server ships with predefined definitions for several common protein sequence databases. Database Manager is a browser-based utility for configuring and updating local copies of sequence databases. For troubleshooting purposes, it can be helpful to understand the low-level operations with FASTA files, described in Manual Configuration and Updating.
Contaminants
If you search a single organism database, it is usually a good idea to include sequences for common contaminants, such as keratins, BSA, and trypsin. Mascot Server includes configuration for two contaminants databases.
UniProt definitions
SwissProt
SwissProt is included in every Mascot installation. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions.
TrEMBL and UniRef
UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization.
UniRef (UniProt Reference Clusters) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms).
UniProt proteomes
Selected UniProt proteomes are provided as predefined definitions for convenient one-click install. To enable a predefined proteome:
- Go to your local Mascot home page, Configuration Editor, Database Manager
- Under Fasta, select Enable predefined definition
- Click Enable next to the desired proteome
Any proteome from UniProt can be added as a searchable database. Follow the instructions in Sequence database setup: UniProt proteomes.
| Database name | Organism | Taxonomy ID | Uniprot ID | Coverage |
|---|---|---|---|---|
| UP6548_A_thaliana | Arabidopsis thaliana (Mouse-ear cress) (Strain: cv. Columbia) | 3702 | UP000006548 | 99.6% |
| UP9136_B_taurus | Bos taurus (Bovine) (Strain: Hereford) | 9913 | UP000009136 | 98.0% |
| UP1940_C_elegans | Caenorhabditis elegans (Strain: Bristol N2) | 6239 | UP000001940 | 99.7% |
| UP6906_C_reinhardtii | Chlamydomonas reinhardtii (Chlamydomonas smithii) (Strain: CC-503) | 3055 | UP000006906 | 96.0% |
| UP437_D_rerio | Danio rerio (Zebrafish) (Brachydanio rerio) (Strain: Tuebingen) | 7955 | UP000000437 | 96.9% |
| UP2195_D_discoideum | Dictyostelium discoideum (Slime mold) (Strain: AX4) | 44689 | UP000002195 | 96.0% |
| UP803_D_melanogaster | Drosophila melanogaster (Fruit fly) (Strain: Berkeley) | 7227 | UP000000803 | 99.3% |
| UP625_E_coli_K12 | Escherichia coli (strain K12) (Strain: K12 / MG1655 / ATCC 47076) | 83333 | UP000000625 | 100.0% |
| UP219602_F_oxysporum | Fusarium oxysporum f. sp. radicis-cucumerinum (Strain: Forc016) | 327505 | UP000219602 | 98.5% |
| UP317484_G_aquaeductus | Geodermatophilus aquaeductus (DSM 46834) | 1564161 | UP000317484 | 99% |
| UP5640_H_sapiens | Homo sapiens (Human) | 9606 | UP000005640 | 99.5% |
| UP589_M_musculus | Mus musculus (Mouse) (Strain: C57BL/6J) | 10090 | UP000000589 | 99.7% |
| UP254291_M_gilvum | Mycolicibacterium gilvum (NCTC10742) | 1804 | UP000254291 | 99.2% |
| UP808_M_pneumoniae | Mycoplasma pneumoniae (strain ATCC 29342 / M129) | 272634 | UP000000808 | 75.9% |
| UP59680_O_sativa | Oryza sativa subsp. japonica (Rice) (Strain: cv. Nipponbare) | 39947 | UP000059680 | 87.0% |
| UP8311_R_communis | Ricinus communis (Castor bean) | 3988 | UP000008311 | 90.5% |
| UP2494_R_norvegicus | Rattus norvegicus (Rat) (Strain: Brown Norway) | 10116 | UP000002494 | 97.8% |
| UP2311_S_cerevisiae | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker’s yeast) | 559292 | UP000002311 | 98.9% |
| UP2485_S_pombe | Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) | 284812 | UP000002485 | 97.8% |
| UP8227_S_scrofa | Sus scrofa (Pig) (Strain: Duroc) | 9823 | UP000008227 | 96.2% |
| UP241690_T_harzianum | Trichoderma harzianum CBS 226.95 | 983964 | UP000241690 | 98.6% |
| UP5226_T_rubripes | Takifugu rubripes (Japanese pufferfish) (Fugu rubripes) | 31033 | UP000005226 | 95.2% |
| UP279841_T_thermophilus | Thermus thermophilus | 274 | UP000279841 | 85.5% |
| UP186698_X_laevis | Xenopus laevis (African clawed frog) (Strain: J) | 8355 | UP000186698 | 95.6% |
| UP7305_Z_mays | Zea mays (Maize) (Strain: cv. B73) | 4577 | UP000007305 | 96.4% |
EST databases
The EST Fasta files from EMBL contain “single-pass” cDNA sequences, or Expressed Sequence Tags. The sequences are divided into 10 divisions, which are available as predefined definitions.
Custom databases
Mascot Server can use any nucleic acid or protein sequence database in FASTA format. Finding sequence databases lists common repositories of protein sequences.
Spectral libraries
Mascot Server includes several predefined definitions for spectral libraries in NIST MSP format. For example:
To enable a predefined spectral library:
- Go to your local Mascot home page, Configuration Editor, Database Manager
- Under Library, select Enable predefined definition
- Click Enable next to the desired library
Discontinued databases
Several protein sequence databases have been discontinued over the years. The configuration notes are archived here for historical purposes.