aselcrit.html

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.

SEL_KEYWORDS :

To select sequences from keyword(s)

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.

SEL_LIST :

To use a previously defined list in building a new query

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.

SEL_REFERENCE :
To select from a bibliographic reference

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Unpublished, or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.

SEL_AUTHOR :
To select from author(s) last 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.

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

SEL_JOURNAL :
To select sequences published in a given journal

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

SEL_NAME :
To select from sequence name(s)

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@

SEL_ACCESSION :
To select from an accession number

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

SEL_TYPE :
To select sequences of a given 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). 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.

SEL_YEAR :
To select sequences published in a given year

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.

SEL_ORGANELLE :
To select sequences encoded in a particular organelle

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.

SEL_MOLECULE :
To select sequences of a given 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.

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.

SEL_SEQFILE :
To retrieve sequences whose names are in a file.

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.

SEL_ACCFILE :
To retrieve sequences whose accession numbers are in a file.

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.

SEL_STATUS :
To select sequences of a given status

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.

SEL_SPECFILE :
To build a list of species from a series of names present in a file.

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.

SEL_KEYFILE :
To build a list of keywords from a series of names present in a file.

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.

The current logfile name appears on top of panel Logging to file.

SEL_SPECIES :

To select sequences from species or taxa name(s)

SEL_KEYWORDS :

To select sequences from keyword(s)

SEL_LIST :

To use a previously defined list in building a new query

SEL_REFERENCE :
To select from a bibliographic reference

SEL_AUTHOR :
To select from author(s) last name

SEL_JOURNAL :
To select sequences published in a given journal

SEL_NAME :
To select from sequence name(s)

SEL_ACCESSION :
To select from an accession number

SEL_TYPE :
To select sequences of a given type

SEL_YEAR :
To select sequences published in a given year

SEL_ORGANELLE :
To select sequences encoded in a particular organelle

SEL_MOLECULE :
To select sequences of a given molecule

SEL_SEQFILE :
To retrieve sequences whose names are in a file.

SEL_ACCFILE :
To retrieve sequences whose accession numbers are in a file.

SEL_STATUS :
To select sequences of a given status

SEL_SPECFILE :
To build a list of species from a series of names present in a file.

SEL_KEYFILE :
To build a list of keywords from a series of names present in a file.

LOG_TEXT_WIDOW :

LOG_ALL_LIST :

SET_LOG_FILENAME :

SEL_SPECIES : To select sequences from species or taxa name(s)

SEL_SPECIES :

To select sequences from species or taxa name(s)