Documentation
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Overview ¶
Package align provides functionality for aligning sequences.
Alignment Steps ¶
Alignments are represented as Steps. Each step when aligning two sequences can be either taking a character from each sequence and aligning them together, or taking only one character and aligning it with a gap. The match step covers the case of a mismatch as well.
For example, the alignment of "blablab" and "blrblbr":
blablab- || || | blrbl-br
Can be represented in steps as:
[match, match, match, match, match, deletion, match, insertion]
Index ¶
Constants ¶
const Gap = 255
Gap is the byte value for a gap in a substitution matrix.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Step ¶
type Step byte
A Step is an alignment of one character from each sequence.
const ( Match Step = 1 // A character of A is aligned with a character of B. Deletion Step = 2 // A character of A is aligned with a gap. Insertion Step = 3 // A character of B is aligned with a gap. )
Possible values of a step.
func Global ¶
func Global(a, b []byte, m SubstitutionMatrix) (steps []Step, score float64)
Global performs global alignment on a and b and finds the highest scoring alignment. Returns the steps relating to a, and the alignment score. Time and space complexities are O(len(a)*len(b)).
Uses the Needleman-Wunsch algorithm.
func Local ¶ added in v0.1.13
func Local(a, b []byte, m SubstitutionMatrix) ( steps []Step, ai, bi int, score float64)
Local performs local alignment on a and b and finds the highest scoring alignment. Returns the steps relating to a, ai and bi as the start positions of the local alignment in a and b respectively, and the alignment score. Time and space complexities are O(len(a)*len(b)).
Uses the Smith-Waterman algorithm.
type SubstitutionMatrix ¶
A SubstitutionMatrix is a map from character pair p to the score of aligning p[0] with p[1]. Character 255 is reserved for gap. The pair [Gap,Gap] represents the general cost of opening a gap (gap-open). A matrix may be asymmetrical.
var ( Levenshtein SubstitutionMatrix // Returns negated edit distance. PAM120 SubstitutionMatrix PAM160 SubstitutionMatrix PAM250 SubstitutionMatrix BLOSUM80 SubstitutionMatrix BLOSUM62 SubstitutionMatrix BLOSUM45 SubstitutionMatrix )
func (SubstitutionMatrix) Get ¶
func (m SubstitutionMatrix) Get(a, b byte) float64
Get returns the value of aligning a with b. Either argument may have the value Gap. Panics if the pair [a,b] is not in the matrix.
func (SubstitutionMatrix) GoString ¶ added in v0.1.12
func (m SubstitutionMatrix) GoString() string
GoString implements the fmt.GoStringer interface.
func (SubstitutionMatrix) Symmetrical ¶
func (m SubstitutionMatrix) Symmetrical() SubstitutionMatrix
Symmetrical returns a copy of m. The copy also contains each pair flipped, mapped to the pair's original value.
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