WWW-Query Help

Use of the buttons

In the following order, you should:
  1. Select the type of search (Use the button "Search for sequences" to retrieve a set of sequences, or "Search for families" to retrieve a set of families. If you select the "family" button, only the databases containing gene families will be available in the list),
  2. Select the type of sequences (Use the button "Protein" to select a database which contains proteins, or the button "Nucleotide" to select a database which contains nucleotide sequences), then
  3. Choose the database.
Afterwards you can enter several (up to 4) selection criteria and submit your request.

Databases

This field allows to select one of the proposed databases with a radio button. Up to now, these databases are: EMBL, GenBank, SWISS-PROT/TREMBL, NBRF, Hovergen Nucl., Hovergen Prot., Hobacgen Nucl., Hobacgen Prot., NuReBase Nucl., NuReBase Prot., NRSub, EMGLib, and HAMAP.

Use the button 'protein databank' or 'nucleotide databank' to select databases containing protein sequences (Swiss-Prot, PIR, etc.) or nucleotide sequences (EMBL, GenBank, EMGLib, NRSub,etc.). Some databases (Hobacgen, Hovergen, NureBase, RTKdb, HoGenom, etc.) present both a protein and a nucleotide database.

Selection Criteria

Many selection criteria are available. Mainly they correspond to the structured elements of the sequence documentation in the data banks.

Keyword

Enter the keyword name, using @ to specify any series of characters to catch several keywords in one shot. Use of space is allowed. Examples: RNA POLYMERASE, @POLYMERASE, @TRANSFER RNA@SYNTHETASE@. Keywords are partially tree-structured. Any match catches also all keywords placed below in the tree.

Keywords_lst

Give the name of a keywords list you have transferred to the server, this using the send a list utility.

Reference

Enter the reference name. References are specified as follows depending on the type of document: 

Document          Format                          Example

Journal article   journal_code/volume/1st_page    jme/34/17
Book              book/year/1st_author            book/1980/broker
Thesis            thesis/year/1st_author          thesis/1984/wildgruber
Patent            patent/patent_coded_number      patent/ep0238993
Unpublished, or
  submitted       unpubl/year/1st_author          unpubl/1993/cho

Author

Enter an author name, possibly using @ to match any string of characters (slow). Examples: YANOFSKI, YANOF@. Only last names are indexed - initials are ignored. All authors of journal articles are indexed. Only the first author of books, theses, patents and other documents are indexed.

Journal

Enter a journal code. The list of all journals codes in EMBL, GenBank, NBRF, SWISS-PROT, Hovergen, NRSub, and EMGLib can be consulted here.

Name

Enter a sequence name, possibly using @ to match any string of characters. Use of @ is VERY slow when placed at the beginning of the query, otherwise the reply is fast. Examples: ECTRPA, ECTRP@.

Names_lst

Enter the name of a list containing sequence names. For that purpose you may either use a list previously created with WWW-Query or a list you have sent with the send a list utility.

Access.

Enter an accession number. Example: L04470. All accession numbers listed in sequence annotations are indexed.

Access_lst

Enter the name of an list containing sequence accession numbers you have transferred to the server, this with send a list utility.

Type

Sequence type identifies the nature of the encoded molecule (e.g., protein, tRNA, rRNA). Type should not be confused with molecule which denotes the chemical nature of the sequenced molecule (e.g., DNA, mRNA, tRNA). Type is defined only for the nucleotide sequence banks (GenBank, EMBL, Hovergen, NRSub and CGDB). Presently the existing types are: 
    ID            Locus entry                (EMBL, SWISS-PROT, NRSub)
    LOCUS         Locus entry                (GenBank, Hovergen, EMGLib)
    CDS          .PE protein coding region   (all)
    RRNA         .RR mature ribosomal RNA    (all)
    TRNA         .TR mature transfer RNA     (all)
    MISC_RNA     .RN other structural RNA
                  coding region              (EMBL, GenBank, Hovergen, NRSub,
                                              EMGLib)
    SNRNA        .SN small nuclear RNA       (EMBL, GenBank, Hovergen, EMGLib)
    SCRNA        .SC small cytoplasmic RNA   (EMBL, GenBank, Hovergen, NRSub,
                                              EMGLib)
    3'INT        .3I 3' intron               (Hovergen)
    3'NCR        .3F 3' non-coding region    (Hovergen)
    5'INT        .5I 5' intron               (Hovergen)
    5'NCR        .5F 5' non-coding region    (Hovergen)
    CPG          .CG region > 200 bp with
                  CpGobs/CpGexp > 0.5        (Hovergen)
    INT_INT      .IN internal intron         (Hovergen)
Each entry of a FEATURE TABLE describing a coding region of a DNA fragment gives rise to a subsequence equal to the fragments described in the location of the feature. The type of the resulting subsequence equals the key of the corresponding feature table entry. The name of the resulting subsequence is built by adding to the parent sequence's name an extension uniquely identifying this particular feature.

Sequences of a given type are generally subsequences, i.e., fragments of parent sequences, except if the coding region covers totally the parent sequence, in which case ACNUC does not create a subsequence.

Year

Type the desired year of publication in the box, with one of these operations: > (after), = (this year), or < (before).

Species

Enter the species name, using @ to specify any series of characters to catch several keywords in one shot. Use of space is allowed. Examples: ESCHERICHIA COLI, @COLI, E@COLI. Species names are tree-structured according to the biological classification of species.

Organelle

Organelle (e.g., chloroplast, mitochondrion) denotes the nature of the genome that harbors a particular gene. By extension, WWW-Query also sees `nuclear' as an organelle. Also, a nuclear-encoded gene coding for a protein imported to an organelle is seen as a nuclear gene by WWW-Query. The existing organelles are: 
    CHLOROPLAST     Chloroplast genome   (EMBL, GenBank, NBRF, Hovergen)
    MITOCHONDRION   Mitochondrial genome (EMBL, GenBank, NBRF, Hovergen)
    KINETOPLAST     Kinetoplast genome   (EMBL, GenBank, Hovergen)
    NUCLEAR         Nuclear genome       (all)

Molecule

In ACNUC, molecule denotes the chemical nature of the sequenced molecule (e.g., DNA, mRNA, tRNA). Molecule should not be confused with type which identifies the encoded molecule (e.g., protein, tRNA, rRNA). Thus the sequence of a tRNA gene has DNA for molecule because DNA rather than tRNA was sequenced. The subsequence covering the tRNA region has tRNA for type because this is the nature of the encoded product. Molecule is defined only for the nucleotide sequence banks (GenBank, EMBL, Hovergen, NRSub, and CGDB). Presently the existing molecules are: 
    DNA          Sequenced molecule is DNA   (all)
    RNA          Sequenced molecule is RNA   (all)
    MRNA         Sequenced molecule is mRNA  (GenBank, Hovergen)
    RRNA         Sequenced molecule is rRNA  (GenBank, Hovergen)
    URNA         Sequenced molecule is tRNA  (GenBank, Hovergen)
    URNA         Sequenced molecule is snRNA (GenBank, Hovergen)

Status

Status denotes the completion level of sequence annotations. This information exists only with the data banks in EMBL or SWISS-PROT formats. The existing status are: 
    PRELIMINARY         Preliminary annotated sequence
    STANDARD            Fully annotated sequence
    UNANNOTATED         Only DE, AC and R[NPXATL]
    UNREVIEWED          Sequence with unreviewed annotation

Logical Operators

Elementary selection criteria (e.g., by species, by keyword) may be logically combined to create multi-criterion queries using operators. Only one operator is available for the first selection criteria: NOT. The default option, DEFAULT, has no effect on the query and is present only for aesthetic purpose. For the three other criteria, four operators are available: AND, OR, AND NOT, OR NOT.

List Name

Under WWW-Query, the result of each query is saved in a file stored locally on our server. By this way, it is not immediatly lost and the user has the possibility to re-use it for building other queries or for performing treatments.The lists defined by the user are stored in a sub-directory of /ftp/ftpdir/pub/ADE-User/data/ created for the user, as defined here.It is up to the user to give a name to a list. If no name is given, the system uses by default list. Be aware than some lists are created automatically by the system. These lists are always called list and erase the lists previously defined with this name.
Note that files older than 1 week in the directory created by the user are automatically cleaned.

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