Select Sequence
Choosing Select... Sequence
opens an interface for selecting residues by entering a specific sequence
or pattern of amino acids or nucleotides.
To instead display an entire sequence and select segments within it with
the mouse, use the
Sequence tool.
The sequence selection dialog has two sections arranged as index cards;
clicking the tab for a card brings it to the front.
-
The Subsequence section allows the sequence to be specified
as a string of one-letter codes. Case is not important.
Ambiguity codes may be used:
- none - only allow exact matches of one-letter codes
- protein - in addition to exact one-letter code matching,
allow B to match aspartic acid (D) and asparagine (N)
and Z to match glutamic acid (E) and glutamine (Q)
- nucleic acid - in addition to exact one-letter code matching,
allow R to match the standard purine nucleotides (A, G), Y to match the
standard pyrimidine nucleotides (C, T, U), and N to match any of the five
(A, C, G, T, U)
-
The PROSITE pattern section allows the sequence to be specified with
PROSITE pattern syntax. Residue codes must be
capitalized; extended syntax involving an asterisk,
e.g. <{C}*>, is not supported.
Note that occurrences in all sequence types (protein, DNA, and RNA)
will be considered matches unless the option to
Force interpretation... as protein or nucleic acid sequence is on.
When the option is on, only sequences of the indicated type
will be examined for matches.
Multalign Viewer can perform
similar searches within a sequence alignment.
UCSF Computer Graphics Laboratory / March 2023