SequenceAlignmentTable

SequenceAlignmentTable[sequence1,sequence2]⟹summary

returns a table showing sequence similarity, identity, gaps, and a visual preview of the alignment betwen sequence1 and sequence2.

Details

SequenceAlignmentTable extends upon the functionality of the native Mathematica SequenceAlignment[] function.
Sequence identity is calculated by dividing by the length of the total aligned sequence, including gaps.

Input

Output

General Options

Examples

Basic Examples (4)

Align two string sequences and show a summary of the alignment:

Align a string sequence with an explicitly typed sequence:

Align a known sequence with the sequence linked to a DNASequencing data object:

Align a known sequence with the sequence linked to a DNASequencing analysis object:

Options (11)

GapPenalty (2)

By default, the GapPenalty is zero and a global alignment is used. If one sequence is much shorter than the other, this shorter sequence can be substantially fragmented in the alignment:

Increasing the GapPenalty reduces the number of discontinuous gaps in the alignment at the expense of decreasing the number of matches:

Method (2)

Set Method to NeedlemanWunsch to do a global alignment using NeedlemanWunschSimilarity[]:

Set Method to SmithWaterman to do a local alignment using SmithWatermanSimilarity[]:

OutputFormat (3)

OutputFormat defaults to Table which shows a summary of the alignment:

Set OutputFormat to List to return a list of computed quantities:

The listed OutputFormat is useful when alignment results are needed in other calculations:

PreviewLineWidth (2)

Set the maximum number of characters to show on each line of the graphical preview:

The default PreviewLineWidth is 60:

SimilarityRules (2)

The default similarity rules are {{a_, a_} -> 1, {a_, b_} -> -1}, which assigns a score of 1 to matches and -1 to mismatches. SequenceAlignmentTable aligns sequences by maximizing this score:

Ruin your alignment by favoring mismatches and penalizing matches:

Messages (1)

InvalidInputSequence (1)

Error shows if a sequence could not be resolved from one or more inputs: