In the following order, you should:
Afterwards you can enter several (up to 4) selection criteria and submit your
This field allows to select one of the proposed databases with a
radio button. Up to now, these databases are:
- 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
- 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
- Choose the database.
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.
Many selection criteria are available. Mainly they correspond to the structured
elements of the sequence documentation in the data banks.
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.
Give the name of a keywords list you have transferred to the server, this
using the send a list utility.
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
submitted unpubl/year/1st_author unpubl/1993/cho
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.
Enter a journal code. The list of all journals codes in
can be consulted here.
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@.
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.
Enter an accession number. Example: L04470. All accession numbers
listed in sequence annotations are indexed.
Enter the name of an list containing sequence accession numbers you have
transferred to the server, this with send a list
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,
SNRNA .SN small nuclear RNA (EMBL, GenBank, Hovergen, EMGLib)
SCRNA .SC small cytoplasmic RNA (EMBL, GenBank, Hovergen, NRSub,
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.
Type the desired year of publication in the box, with one of these operations:
> (after), = (this year), or < (before).
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 (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)
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 denotes the completion level of sequence annotations. This
information exists only with the data banks in EMBL or SWISS-PROT
The existing status are:
PRELIMINARY Preliminary annotated sequence
STANDARD Fully annotated sequence
UNANNOTATED Only DE, AC and R[NPXATL]
UNREVIEWED Sequence with unreviewed annotation
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.
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
If you have problems or comments...
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