|
LINE-LENGTH number | 50
SEGMENT-LENGTH number | 10 SHOW-CONSENSUS TRUE | FALSE TO-VARIABLE TRUE | FALSE |
AS NAME | VALUE | ANY
IN organism VERBOSE TRUE | FALSE |
Example:
- Aligns and displays a list of sequences
- List may consist of any combination of:
* Frame names (e.g. #$A7120.all4312)
* Names in string (e.g. "A7120.all4312")
* Short names (e.g. all4312)
* Symbols of name or short name (e.g. 'all4312)
* Variables holding one or more reference to a gene or protein
* Strings containing nucleotide or amino acid sequences- The alignment is displayed with the specified line-length (default 50)
- Each line is shown as segments of segment-length (default 10).
This is useful, for example, to display codons in an open reading frame
(setting segment-length to 3).- The sequences are followed by consensus symbols unless SHOW-
CONSENSUS is set to FALSE- If TO-VARIABLE is set to TRUE (default FALSE), then the alignment
is not displayed but is instead returned as a list of the form:
((name-of-sequence aligned-sequence)
(name-of-sequence aligned-sequence)
...
("consensus" consensus-line))
(ALIGNMENT-OF (ALL-ORTHOLOGS-OF p-all4312))
[Result is an amino-acid alignment of all orthologs of all4312 (including all4312 itself)]
Example:
(ALIGNMENT-OF (ALL-ORTHOLOGS-OF all4312) LINE-LENGTH 60 SEGMENT-LENGTH 3)
[Result is a nucleotide alignment of all orthologs of all4312 (including all4312 itself)
Nucleotides are grouped in three's to make codons more evident]