|
THRESHOLD number
MISMATCHES positive integer RETURN positive integer |
AS NAME | VALUE | ANY
IN organism VERBOSE TRUE | FALSE |
Example:
- Returns the sequence of the given gene, protein, contig, replicon, or genome
- These entities may be specified as:
* A name of a gene, protein, contig, or replicon
* A variable holding one of the above
* A list holding any combinations of the above- If FROM, TO, or LENGTH are not specified, then entire sequence is returned
- If FROM alone is specified, then sequence from that coordinate to end is returned (circularity of replicon is ignored)
- If TO alone is specified, then sequence from beginning to that coordinate is returned (circularity of replicon is ignored)
- If FROM and LENGTH are both specified, then a sequence of the specified length is returned, beginning from the FROM coordinate
- If LENGTH alone is specified, then a sequence of the specified length is returned, beginning from the start of the entity
- FROM and TO are calculated from the beginning of the entity and, in the case of genes, may go beyond the limits of the entity (negative TO coordinate is allowed), resulting in upstream or downstream sequence being returned.
- If START-OFFSET is specified, then the sequence returned begins with the given number of nucleotides offset from the beginning of the entity
- If END-OFFSET is specified, then the sequence returned ends with the given number of nucleotides offset from the end of the entity
- If INVERT is set to TRUE, then gene sequences are returned as the reverse complement
(SEQUENCE-OF pNpA)
[Result is the entire sequence of the plasmid]
Example:
(SEQUENCES-OF (ORTHOLOGS-OF all4312) START-OFFSET -50 LENGTH 100)
[Result is the 100 nucleotides spanning the beginning of each gene orthologous to all4312]