Talk:Smith–Waterman algorithm

message: Referring back to the 1981 paper of Smith and Waterman (ftp://150.128.97.71/pub/Bioinformatica/msw-042.pdf, formula (1)), the definition formula for the cells of the matrix H is not the same as in this article.  The gap scores do not only depend on the row above and the column to the left; they depend on all rows above and all columns to the left.  There are examples where this makes a difference to the final score, so the definition here is not correct.
An example:  Reference:
AACCCGAGTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAAAGCAATGGCAAGAATTGGAATGGAAAGGAATC
Read:
GAATGGAATGGAATGCAATGGAATGGAATCATCCGTAATGGAATGGAAAGCAATGGAATG
Scoring +2 for match, -6 for mismatch, -5 for gap open, -3 for gap extend, the overall score is 66 by Smith-Waterman's algorithm and 62 by the algorithm presented here.  — Preceding unsigned comment added by 217.33.180.66 (talk) 13:15, 17 March 2014 (UTC)
thread_title:  Wrong formula for matrix? 

message: 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)
thread_title: WPMED

message: 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)
thread_title:  Pseudocode of Algorithm and Remarks to Code are missing 

message: 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\le i\le m, 1\le j\le 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\le i\le m, 1\le j\le 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)
thread_title:  Eq. -- why the 0? 

message: I find this article similar to post with "me faster" signs. As someone who actually takes part in "competition" of speeding up Smith-Waterman for different architectures I think it's a bit NPOV. (disclaimer: i haven't add mine implementation yet to the article but I intend to do so).
Performance results should be reported not as a single value but a graph with performance plotted against query size and database used. For example Fastflow implementation achieves 35GCUPS for __very__ long queries that are barely if ever used in practice. I think it's a bit misleading.
I guess that I'll rewrite this article and put pefrormance graph for different algorithms. But it would be nice if someone reviewed the article afterwards (coz I'll add my own work on SW too) to eliminate potential NPOV.
Crenshaw (talk)  —Preceding undated comment added 22:20, 30 January 2010 (UTC)
replies: text: Agree. The "754x speedup" is meaningless - compared to what? Ketil (talk) 21:32, 11 December 2011 (UTC)
thread_title:  Performance reports 

message: As a commenter above points out, this example is not good. The example in the article currently results in a local alignment which is also a global alignment. As the whole point of Smith-Waterman is to find the best local alignment, the example should find the best alignment of the best matching substring(s) in the 2 strings. I don't have time to fix this right now, but wanted point that out. --Rajah (talk) 03:46, 23 March 2010 (UTC)
replies: text: I'd also like a better example, or perhaps two examples, a simple one, and a longer one. I am having a hard time understanding how the algorithm works. What I have gathered so far is that it will build a matrix, and this matrix has the optimal alignment. But from this part, how to get the optimal sequence, is not completely clear to me. 2A02:8388:1641:8D00:BE5F:F4FF:FECD:7CB2 (talk) 15:44, 28 May 2016 (UTC)
thread_title: Example needs to totally be redone

message: Please: As you see, and en-dash rather than a hyphen is used in the title of this article, and of course should also be used in the body of the article.  I just cleaned up a lot of that.  Similarly, "Needleman-Wunsch" is wrong and "Needleman–Wunsch" is right.  (Also in ranges of pages, years, etc., e.g.: pp. 305–42.  See WP:MOS. Michael Hardy (talk) 17:25, 7 August 2012 (UTC)
thread_title:  en-dashes 

message: The first reference to the paper in PDF seems to be dead, it looks like the university blocked it. There is another copy in here http://www.cmb.usc.edu/papers/msw_papers/msw-042.pdf but I'm not sure if putting that (or for that matter the link to the PDF that was here before) would involve copyright infringement. Can somebody enlighten me about this? Jorgeng87 (talk) 19:21, 13 November 2012 (UTC)
thread_title:  Dead reference 

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message: The implementation section needs to be redone (maybe merged with the section "Accelerated versions"). Unfortunately I'm not familiar with those implementations. I would appreciate it if someone can help rewrite those two sections. It'll help people better use the algorithm.
Yz cs5160 (talk) 18:17, 23 October 2017 (UTC)
thread_title:  Implementation 

message: The intro paragraph says "cubic", which seems to match the pseudocode.
The box on the right says O(mn).
The history mentions cubic again, but points out to *different* algorithms that run in quadratic time (Gotoh and Altschul et al.).
Finally, under "Gap Penalty" one can see that the latter algorithms only solve an (important) special case of the problem, and the former doesn't even necessarily solve it!
Aviad.rubinstein (talk) 21:28, 7 September 2018 (UTC)
thread_title:  Running time: quadratic or qubic??