SEL_SPECIES :
To select sequences from species or taxa name(s)
- Enter the taxon name
- Using @ to specify any series of characters.
Examples:
homo sapiens
rodentia
herpes simplex@
- Press make list (or hit return key) to create the list of matching sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
- The Species browser allows to navigate in the biological classification of species, to find the desired taxon name, and to select attached sequences.
- Enter the keyword name
- Using @ to specify any series of characters to catch
several keywords in one shot.
Exemple :
rna polymerase
@polymerase
@transerf rna@synthetase@
Keywords are partially tree-structured. Any match catches also all keywords
placed below in the tree.
- Press make list (or hit return key) to create the list of matching sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
- The Keywords browse allows to see exactly what keywords match and to select attached sequences.
- Click in the list of lists shown on the desired list.
- Click on build query (or hit return key) to enter this list in the query being built.
- Enter the reference name.
- Press make list (or hit return key) to create the list of matching sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
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Unpublished, or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
Notes:
The codes of largely circulated journals are their well known abbreviations
(e.g., NAR for nucleic acids research, PNAS for Proc. Natl. Acad Sci. USA, JMB
for J. Mol. Biol.)
Codes can easily be found using the browser started by the Journal.
When the year was not found by the indexing software, it is 0.
- Press make list or hit return key to create the list of matching sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Enter an author name, possibly using @ to match any string of characters (slow).
(ex: @DORMOND for Van Dormondt).
Notes:
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
- Click on the desired journal in the scrolling list shown.
You can also type in the box at top the first few letters of the journal name.
- Press make list or hit return key to create the list.
Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Codes other than journal names:
BOOK THESIS UNPUB PATENT
- Press make list or hit return key to create the list of matching sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
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 rapid.
Examples:
ectrpa
ectrp@
- Press make list (or hit return key) to create the list of matching sequences.
Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
All accession numbers listed in sequence annotations are indexed.
Example:
m00001
.
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).
Each entry of a FEATURE TABLE describing a coding region of a DNA
fragment (i.e., CDS, tRNA, rRNA, MISC_RNA, snRNA, scRNA) 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.
Other feature entries (e.g., mRNA, exon, etc...) do not correspond to
subsequences. These may be extracted, though, using option extract feature
of button extract seqs.to file .
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 ACNUCdoes not create a subsequence.
- Click on the desired type in the list shown.
- Press make list or hit return key to create the list.
Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Type the desired year in the box, choose one of the operations:
Y>= (after) = (this year) or <= (= (before).
- Press make list (or hit return key) to create the list.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Each reference of a sequence has a year. Thus a sequence with several references
may appear as published in several different years.
Organelle (e.g., chloroplast, mitochondrion) denotes the nature of the genome
that harbors a particular gene. By extension, ACNUC also sees nuclear as
an organelle.
A nuclear-encoded gene coding for a protein imported to an organelle is seen
as a nuclear gene by acnuc.
Click on the desired organelle in the list shown.
- Press make list (or hit return key) to create the list.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
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.
- Click on the desired molecule in the list shown.
- Press make list (or hit return key) to create the list.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
- Type the file name, or press use file browser to retrieve graphically
the file name.
- Press make list (or hit return key) to create the list of given sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Useful files here are typically created by button save list, but may be
created by any other means. They should contain one sequence (or subsequence)
name by line and nothing else.
Loading a file of several hundred names may take a while.
- Type the file name, or press use file browser to retrieve graphically
the file name.
- Press make list (or hit return key) to create the list of given sequences.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Useful files here are typically created by button save list, but may be
created by any other means. They should contain one accession number
by line and nothing else.
Loading a file of several hundred lines may take a while.
Status denotes the completion level of sequence annotations.
In GenBank, this comes from STANDARD lines of the annotations.
In EMBL this comes from the second field of ID lines.
- Click on the desired status in the list shown.
- Press make list (or hit return key) to create the list.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
This operation produces a list of species (rather than a list of sequences!).
- Type the file name, or press use file browser to retrieve graphically
the file name.
- Press make list (or hit return key) to create the list of given species.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Species lists can be turned into sequence lists by operator proj. to seq.
Sequence lists can be turned into species lists by operator proj. species
Useful files here are typically created by button save list applied to a
list of species but may be created by any other means. They should contain one
species name by line and nothing else.
This operation produces a list of keywords (rather than a list of sequences!).
- Type the file name, or press use file browser to retrieve graphically
the file name.
- Press make list (or hit return key) to create the list of given keywords.
- Press build query if you wish to compose a query of several criteria
combined with operators such as and, or, not.
Keyword lists can be turned into sequence lists by operator proj. to seq.
Sequence lists can be turned into keyword lists by operator proj. keywords
Useful files here are typically created by button save list applied to a
list of keywords but may be created by any other means. They should contain one
keyword by line and nothing else.
- Copies to the logfile the contents of the text data output panel
- The logfile name (query.log by default) may be changed by pressing the Set filename button.
- Copies to the logfile the output produced by the operation chosen in
panel Choose shown applied to the whole list present in List content
- Progress of this operation is graphically displayed, and may be interrupted
by clicking button interrupt that appears.
- To set the logfile name
- Enter the desired logfile name in the dialog window that appears.
- The current logfile name appears on top of panel Logging to file.