euGenes Search Help

General

Constructing a query.

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 /^[A-Z]+\-(amine|esterase)/

The query semantics are those of SRS, and are more fully documented at SRS manual, for instance.

Fields

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, etc.
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.

Refining queries

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 returned.

Organism selection

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

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

These library designations appear in the results listing description of your query.

Search engine

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 'Everything' field.

Send comments to us at eugenes@iubio.bio.indiana.edu
euGenes uses Argos: A Replicable Genome infOrmation System