Find motifs and complements
With npm:
npm install @rnacanvas/search
All exports of this package can be accessed as named imports.
// some example imports
import { motifSearch, complementsSearch } from '@rnacanvas/search';
function motifSearch()Search for motifs within a sequence.
var motif = 'CUGCCA';
var sequence = 'agCUGCCAugcga';
// returns a collection of match objects
var matches = [...motifSearch(motif, sequence)];
matches.length; // 1
// zero-based index of the match
matches[0].index; // 2
// one-based position of the match
matches[0].position; // 3
// the number of characters in the match
matches[0].length; // 6
Motif search is not case-sensitive.
var motif = 'cugcca';
var sequence = 'agCUGCCAugcga';
[...motifSearch(motif, sequence)].length; // 1
Sequences of bases can also be input to the motifSearch() function instead of strings.
var motif = [...'CUGCCA'].map(c => Nucleobase.create(c));
[...'agCUGCCAugcga'].forEach(c => app.drawing.addBase(c));
[...motifSearch(motif, app.drawing.bases)].length; // 1
[...motifSearch('CUGCCA', app.drawing.bases)].length; // 1
Any sequence of objects fulfilling the TextContent interface (below)
can be input to the motifSearch() function.
interface TextContent {
textContent: string;
}
Note that bases with empty text content or text content containing more than one character won’t be matched with other bases or characters.
Lowering the cutoff value allows for imperfect matches to be returned.
var motif = 'CUGCCA';
var sequence = 'CaGCCA';
// no matches (cutoff is 1 by default)
[...motifSearch(motif, sequence)].length; // 0
[...motifSearch(motif, sequence, { cutoff: 0.8 }].length; // 1
The cutoff value can be “loosely” thought of as the proportion of the motif that must match the sequence for a match to be returned.
Gaps are allowed in matches.
Mismatch and gap penalties can also be specified.
motifSearch('CUGCCA', 'agCUGCCAuca', {
cutoff: 0.9,
mismatchPenalty: -1,
gapPenalty: -1.5,
});
By default, mismatch penalty is -1 and gap penalty is -1.5.
(A matching pair corresponds to +1 and the cutoff value is 1 by default.)
IUPAC nucleic acid codes are also recognized by the motifSearch() function.
var motif = 'CYRCCA';
var sequence = 'aggCcGCCAugccCUaCCAag';
var matches = [...motifSearch(motif, sequence)];
matches.length; // 2
IUPAC code matching rules follow those of the SequenceCharacter class described below.
function complementsSearch()Search for complements to a motif within a sequence.
var motif = 'CUGCCA';
var sequence = 'ucUGGCAGggacugca';
// returns a collection of complement objects
var complements = [...complementsSearch(motif, sequence)];
complements.length; // 1
// zero-based index of the complement
complements[0].index; // 2;
// one-based position of the complement
complements[0].position; // 3
// the number of characters in the complement
complements[0].length; // 6
Complements search is not case-sensitive.
var motif = 'cugcca';
var sequence = 'ucUGGCAGggacugca';
[...complementsSearch(motif, sequence)].length; // 1
Sequences of bases can also be input to the complementsSearch() function instead of strings.
var motif = [...'CUGCCA'].map(c => Nucleobase.create(c));
[...'ucUGGCAGggacugca'].forEach(c => app.drawing.addBase(c));
[...complementsSearch(motif, app.drawing.bases)].length; // 1
[...complementsSearch('CUGCCA', app.drawing.bases)].length; // 1
Any sequence of objects fulfilling the TextContent interface (below)
can be input to the complementsSearch() function.
interface TextContent {
textContent: string;
}
Note that bases with empty text content or text content containing more than one character won’t be complemented with other bases or characters.
Lowering the cutoff value also allows for imperfect complements to be returned.
var motif = 'CUGCCA';
var sequence = 'ucUGcCAGggacugca';
// no complements (cutoff is 1 by default)
[...complementsSearch(motif, sequence)].length; // 0
[...complementsSearch(motif, sequence, { cutoff: 0.8 }].length; // 1
The cutoff value “loosely” corresponds to the proportion of the motif that must be complementary to the sequence for a complement to be returned.
Gaps and G:U / G:T pairs are allowed in complements.
Mismatch, gap and wobble penalties can also be specified.
complementsSearch('CUGCCA', 'ugUGGCAGgga', {
cutoff: 0.9,
mismatchPenalty: -1,
gapPenalty: -1.5,
wobblePenalty: -0.5,
});
By default, mismatch penalty is -1, gap penalty is -1.5 and wobble penalty is -0.5.
(Wobble penalty applies to any G:U or G:T pairs in complements.)
A complementary pair in a complement corresponds to +1
and the cutoff value is 1 by default.
IUPAC nucleic acid codes are recognized by the complementsSearch() function.
// Y stands for U or C
var motif = 'CYGCCA';
var sequence = 'caUGGCgGacugg';
[...complementsSearch(motif, sequence)].length; // 1
Rules for complementary pairs are the same as for the SequenceCharacter class described below.
function removeGapCharacters()Returns a new string with all periods and dashes having been removed from the input string.
Removing gap characters can make searching for motifs and complements a simpler task.
removeGapCharacters('.A-GU..C--'); // "AGUC"
removeGapCharacters('---...'); // ""
function removeWhitespace()Returns a new string with all whitespace characters having been removed.
removeWhitespace('A U\tG\nC\rT\r\n'); // "AUGCT"
class SequenceCharacterRepresents a character in a sequence.
var A = new SequenceCharacter('A');
A.toString(); // "A"
A.matches('A'); // true
A.matches('G'); // false
A.complements('U'); // true
A.complements('T'); // true
A.complements('G'); // false
// case doesn't matter
A.matches('a'); // true
A.complements('u'); // true
// IUPAC codes are recognized
A.matches('R'); // true
This constructor will throw for strings that are not composed of a single character.
// empty string
new SequenceCharacter(''); // throws
// more than one character
new SequenceCharacter('AG'); // throws
new SequenceCharacter('asdf'); // throws
A SequenceCharacter instance may be created for any character, though.
toString()Returns the character as a string.
var A = new SequenceCharacter('A');
A.toString(); // "A"
// preserves case
var r = new SequenceCharacter('r');
r.toString(); // "r"
matches()Returns true if the character matches the input character.
var A = new SequenceCharacter('A');
A.matches('A'); // true
A.matches('C'); // false
// case doesn't matter
A.matches('a'); // true
// works for sequence character instances too
A.matches(new SequenceCharacter('A')); // true
IUPAC nucleic acid codes are recognized.
var A = new SequenceCharacter('A');
A.matches('R'); // true
A.matches('Y'); // false
var N = new SequenceCharacter('N');
// the any character matches any non-gap character
N.matches('A'); // true
N.matches('p'); // true
// gap characters
var period = new SequenceCharacter('.');
var dash = new SequenceCharacter('-');
// gap characters only match other gap characters
period.matches('.'); // true
dash.matches('-'); // true
N.matches('.'); // false
N.matches('-'); // false
Returns false for empty strings and strings containing more than one character.
var A = new SequenceCharacter('A');
// empty string
A.matches(''); // false
// strings containing more than one character
A.matches('AG'); // false
A.matches('asdf'); // false
complements()Returns true if the character complements the specified character.
var A = new SequenceCharacter('A');
A.complements('U'); // true
A.complements('A'); // false
// T and U are interchangeable
A.complements('T'); // true
// case doesn't matter
A.complements('u'); // true
// sequence character instances can also be input
A.complements(new SequenceCharacter('U')); // true
IUPAC nucleic acid codes are recognized.
var G = new SequenceCharacter('G');
// since G can pair with C, U and T
G.complements('Y'); // true
var U = new SequenceCharacter('U');
// since U can pair with A or G
U.complements('R'); // true
var N = new SequenceCharacter('N');
// the any character complements any non-gap character
N.complements('A'); // true
// gap characters
var period = new SequenceCharacter('.');
var dash = new SequenceCharacter('-');
// gap characters only complement other gap characters
period.complements('.'); // true
period.complements('-'); // true
N.complements('.'); // false
N.complements('-'); // false
Note that the special IUPAC codes
S, W, K, M, B, D, H and V
have no complements.
This method returns false for empty strings
and strings containing more than one character.
var A = new SequenceCharacter('A');
// empty string
A.complements(''); // false
// strings containing more than one character
A.complements('AG'); // false
A.complements('asdf'); // false
function isWobblePair()Returns true if the two input characters form a G:U or G:T pair.
isWobblePair('G', 'U'); // true
isWobblePair('G', 'T'); // true
isWobblePair('A', 'U'); // false
isWobblePair('G', 'C'); // false
// order doesn't matter
isWobblePair('U', 'G'); // true
// case doesn't matter
isWobblePair('g', 'u'); // true
var G = new SequenceCharacter('G');
var U = new SequenceCharacter('U');
// handles sequence character instances
isWobblePair(G, U); // true
var A = new SequenceCharacter('A');
isWobblePair(A, U); // false
Returns false for empty strings
and strings containing more than one character.
isWobblePair('G', ''); // false
// each string must be a single character
isWobblePair('G', 'UT'); // false