euGenes Search Help
Constructing a query.
The query semantics are those of SRS, and are more fully documented at
SRS manual, for instance.
- In general each word you enter in the search term box is searched,
and all words are combined with a logical 'and' to result in
only those records matching all words.
- Use the logical 'or' word, or '|', to find records matching all
terms in a query.
- Use the logical 'but not' word, or '!', to find records matching
a word but not another word. E.g., find 'adh but not drosophila'.
- Use the '*' asterisk wild card to match any number of letters.
This may be placed anywhere in a phrase, begining or end or middle.
There is a checkbox  which by default adds this wild card to end
of each query.
- Use the '?' question wild card to match an individual letter.
- Full regular expressions can be used inside // slashes, as in
Fields that can be searched include
- Everything - search all words of all fields of gene records.
- Gene symbol/synonym - symbol (short hand name) of gene
and synonyms or aliases if any
- Gene name - full name of gene (not records all have these)
- Gene function - generally function of the enzyme or gene product.
This may be a controlled-vocabulary term or a descriptive phrase.
- Homology - identified gene homology to other organisms, when
known. This can include species, gene symbol in other organism,
and database links showing this homology.
- Phenotype - general descriptions of the phenotype
of a gene.
- Chromosome no. - the chromosome or linkage group number
to which the gene is localized.
- Map position - the cytological, genetic, linkage or other
organism-specific location for the gene on a chromosome.
- Database accession - this includes all database accession
numbers in a gene record, including the reference accession from
which this gene record is summarized,
and other databanks such as PROSITE, PFam, OMIM, GeneCards,
- Gene class - this is a special field which distinguishes
among experimentally determined genes, and those predicted computationally
from sequence data, at present. Use the check box labelled
"excluding [ ] predicted genes" to limit your search to determined
or confirmed genes.
Following the results of a search you will find a form that
allows you to add new field selections and terms to your query.
Use this when you find more results than desired from your
first query. When you select more search words, and new fields
in this refinement form, they are added to your original query,
and the combined result of the original and new query are
Searches can be limited to specific organisms of the euGenes set.
The organism data are indexed as separate libraries, and any
combination of these can be searched using the selector on euGenes
main query page. These libraries are currently denoted as
These library designations appear in the results listing description
of your query.
- FBgn - Fruitfly data library
- HUgn - Human data library
- MGgn - Mouse data library
- ATgn - Weed (Arabidopsis) data library
- CEgn - Worm (C.elegans) data library
- SGgn - Yease (Saccharomyces) data library
- ZFgn - Zebrafish data library
The search software for euGenes is currently based on
Sequence Retrieval System (SRS) v. 5.
Indexing varies for fields, some are indexed as complete
phrases (symbols, some functions).
The euGenes data set can be included in general SRS web servers,
allowing more complex queries of multiple SRS databanks.
See for instance,
IUBio SRS service
All words in a gene record
are also indexed as such and can be searched for with
Send comments to us at
euGenes uses Argos: A Replicable Genome infOrmation System