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File:Needleman-Wunsch pairwise sequence alignment.png

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Needleman-Wunsch_pairwise_sequence_alignment.png (480 × 480 pixels, file size: 36 KB, MIME type: image/png)

Summary

English: The score matrix for an alignment between two nucleotide sequences: 
Sequences    Best Alignments
---------    ----------------------
GCATGCG      GCATG-CG      GCA-TGCG      GCAT-GCG
GATTACA      G-ATTACA      G-ATTACA      G-ATTACA

The Needleman-Wunsch algorithm is a dynamic programming algorithm that finds the best possible alignments between two strings.

It takes three score parameters: match, mismatch, and gap.

Since it is a dynamic programming algorithm, the problem is solved by filling a two dimensional matrix. It requires O(nm) space and time where n and m are the lengths of the first and second string, respectively.

All best possible alignments are found by filling the matrix according to the defined score parameters.

Some optimizations of the algorithm avoid filling values distant from the diagonal, since those values are only needed for the poorest alignments.

Source code: https://gist.github.com/slowkow/508393
Description
English: The score matrix for an alignment between GATTACA and GCATGCU.
Date
Source Own work
Author Slowkow

Licensing

I, the copyright holder of this work, hereby publish it under the following license:
Creative Commons CC-Zero This file is made available under the Creative Commons CC0 1.0 Universal Public Domain Dedication.
The person who associated a work with this deed has dedicated the work to the public domain by waiving all of their rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.

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Date/TimeThumbnailDimensionsUserComment
current20:36, 30 September 2021Thumbnail for version as of 20:36, 30 September 2021480 × 480 (36 KB)GoatsnstoatsChanged last nucleotide to G to be consistent with actual DNA strings
23:35, 22 June 2014Thumbnail for version as of 23:35, 22 June 2014480 × 480 (56 KB)SlowkowReverted to version as of 23:34, 22 June 2014
23:35, 22 June 2014Thumbnail for version as of 23:35, 22 June 2014480 × 480 (50 KB)SlowkowReverted to version as of 23:33, 22 June 2014
23:34, 22 June 2014Thumbnail for version as of 23:34, 22 June 2014480 × 480 (56 KB)Slowkow
23:33, 22 June 2014Thumbnail for version as of 23:33, 22 June 2014480 × 480 (50 KB)Slowkow
02:04, 3 April 2014Thumbnail for version as of 02:04, 3 April 2014480 × 480 (36 KB)SlowkowUser created page with UploadWizard

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