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Query Help



QUERY SEQUENCE PAGE DESCRIPTION

The query page is divided into 5 sections : General, Source, References, Cross-references and Features.

General section

The General section allows to choose the Sequence type. The type of sequence data retrieved from the database depends on it according to the following rule: This section also allows to retrieve entry based on their accesssion number, description, keywords, sequence length or standrad name.
For "keywords" field, you can search more than one keyword and use the AND/OR operators. (AND/OR help)

Source section

The Source section allows to query information related to the source of the sequence (e.g. genotype, isolate, cell line, cell type).
This section allows to select entry based on their genotype/subtype.
The genotypes/subtypes are divided in 3 levels : The lists availble in the form contain all the genotypes/subtypes present in the euHCVdb database.

References section

The References section allows to query data related to journal references (e.g. authors, title word, publication year).
For the Authors fields, there are 3 ways of searching references :

Cross-references section

The Cross-references section allows to query cross-references to external databases (e.g. UniProt or EMBL).

Features section

The Features section allows to perform queries on nucleotide features (e.g. RBS, stem_loop) with or without qualifiers (e.g. function, locus_tag) and protein regions (e.g. HVR1, ISDR, 3D-models).

HOW TO MAKE A QUERY

When performing a query covering more than one criteria, each individual criteria has to be satisfied (intersect).
Example
Extract "e1" protein sequence of isolate "H77" :

Multiple values (+)

Text inputs on the page with "+" allow "multiple criteria" querying.
Multiple values have to be separated by a free space.
Example
Choosing "Genome" in the Sequence type field and "AY754636 AY754639" in the Accession number field will return the complete nucleotide sequences of entries AY754636 and AY754639 found in the database.

"Imprecise" querying

The interface also allows "imprecise" querying by adding "*" before or after a letter (or group of letters).
Example
By choosing "M*" in the Accession number field and "Genome" in the Sequence type field, the query will return all the entries with an accession number starting with the letter M. On the same note, chosing "*5" or "*5*" will return the entries with the accession number ending with "5" or containing "5" respectively.

AND/OR help

Operators "AND" or "OR" (default = "AND") can be used to search more than one keyword. With "AND", the query will return entries with all the query terms present. With "OR", the query will return entries where any of the terms are present.

QUERY 3D-MODELS PAGE DESCRIPTION

The help is describe here.