Sequence database setup: EMBL EST
Overview
The EST Fasta files from EMBL contain "single-pass" cDNA sequences, or Expressed Sequence Tags. The sequences are divided into 10 divisions:
| ENV:Environmental Samples | (predefined: Environmental_EST) |
| FUN:Fungi | (predefined: Fungi_EST) |
| HUM:Human | (predefined: Human_EST) |
| INV:Invertebrates | (predefined: Invertebrates_EST) |
| MAM:Other Mammals | (predefined: Mammals_EST) |
| MUS:Mus musculus | (predefined: Mouse_EST) |
| PLN:Plants | (predefined: Plants_EST) |
| PRO:Prokaryotes | (predefined: Prokaryotes_EST) |
| ROD:Rodents | (predefined: Rodents_EST) |
| VRT:Other Vertebrates | (predefined: Vertebrates_EST) |
Unigene
NOTE: UniGene was retired by NCBI in July 2019, although the final UniGene builds are still available as static content from the FTP site
The NCBI UniGene indexes are created by automatically partitioning GenBank sequences into non-redundant sets of gene-oriented clusters. If UniGene indexes are available locally, results from Mascot searches of EST databases can be grouped and reported by gene family, rather than by raw EST accession numbers.
In Mascot 2.4 and later, the following UniGene indexes are included in the predefined database definitions. To enable UniGene indexes in earlier versions, refer to your local copy of this help page.
- Environmental_EST
- None
- Fungi_EST
- Dictyostelium_discoideum
- Human_EST
- Homo_sapiens
- Invertebrates_EST
- Anopheles_gambiae
- Caenorhabditis_elegans
- Drosophila_melanogaster
- Mammals_EST
- Bos_taurus
- Canis_lupus_familiaris
- Equus_caballus
- Pan_troglodytes
- Sus_scrofa
- Mus_EST
- Mus_musculus
- Plants_EST
- Arabidopsis_thaliana
- Chlamydomonas_reinhardtii
- Hordeum_vulgare
- Oryza_sativa
- Triticum_aestivum
- Zea_mays
- Prokaryotes_EST
- None
- Rodents_EST
- Rattus_norvegicus
- Vertebrates_EST
- Danio_rerio
- Takifugu_rubripes
- Xenopus_laevis
Using the database in Mascot 2.5 and later
In Database Manager, enable the desired EST division from predefined definitions. Database Manager will download the up-to-date configuration information and the sequence database files.
Using the database in Mascot 2.4
Mascot 2.4 does not support HTTPS file downloads. We recommend updating to a later version of Mascot Server.
Using the database in Mascot 2.3 and earlier
Please refer to the local copy of this help page shipped with your version of Mascot Server.
Parse Rules
A typical Fasta title line is:
>EM_EST:AA012645 AA012645.1 RPU0101AC Rat myometrium, differential display Rattus …
Suitable parse rules used by the predefined configuration:
Accession from Fasta title : ">EM_EST:\([A-Z0-9]*\)"
Description from Fasta title : ">[^ ]* \(.*\)"