Talk:Smith–Waterman algorithm

Medicine Start‑class Low‑importance

	Medicine portal This article is within the scope of WikiProject Medicine, which recommends that medicine-related articles follow the Manual of Style for medicine-related articles and that biomedical information in any article use high-quality medical sources. Please visit the project page for details or ask questions at Wikipedia talk:WikiProject Medicine.MedicineWikipedia:WikiProject MedicineTemplate:WikiProject Medicinemedicine
Start	This article has been rated as Start-class on Wikipedia's content assessment scale.
Low	This article has been rated as Low-importance on the project's importance scale.

Template:Wikiproject MCB

WPMED

I am not sure this article falls within the scope of WP:MED. Anyone who agrees, please delete the WPMED tag on this page. --Una Smith (talk) 04:29, 29 December 2007 (UTC)[reply]

Pseudocode of Algorithm and Remarks to Code are missing

There is the simple but efficient pseudocode of the algorithm missing. It is tailored to fit to the properties of genes in common genomes. Maybe someone can link the properties of common (for example eucaryotic cell) genes having introns and exons to the properties of Smith-Waterman or pairwise Smith-Waterman pSW --84.157.243.81 (talk) 09:32, 24 July 2008 (UTC)[reply]

Eq. -- why the 0?

Shouldn't $H(i,j)=\max {\begin{Bmatrix}0&\\H(i-1,j-1)+\ w(a_{i},b_{j})&{\text{Match/Mismatch}}\\H(i-1,j)+\ w(a_{i},-)&{\text{Deletion}}\\H(i,j-1)+\ w(-,b_{j})&{\text{Insertion}}\end{Bmatrix}},\;1\leq i\leq m,1\leq j\leq n$ be $H(i,j)=\max {\begin{Bmatrix}H(i-1,j-1)+\ w(a_{i},b_{j})&{\text{Match/Mismatch}}\\H(i-1,j)+\ w(a_{i},-)&{\text{Deletion}}\\H(i,j-1)+\ w(-,b_{j})&{\text{Insertion}}\end{Bmatrix}},\;1\leq i\leq m,1\leq j\leq n$

What's that zero doing in the B-matrix? —Preceding unsigned comment added by 129.170.215.143 (talk) 23:38, 18 June 2009 (UTC)[reply]

Smith-Waterman is for local alignment, which means that if H(i, j) is 0, then it's best for the alignment to start there. I think the example is really confusing, because it doesn't illustrate this fact, so you get an optimum local alignment that is also a global alignment. 69.218.212.242 (talk) 17:20, 8 August 2009 (UTC)[reply]