Talk:BLAST (biotechnology)

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Untitled

anyone have a citation for BLAST being the most highly cited paper of the 1990s? 152.78.196.32 15:14, 28 September 2006 (UTC)[reply]

What's the relevance of that particular snippet of information, anyway? I vote to have it removed. Stephen 03:16, 7 October 2007 (UTC)== Gumbel distribution ==[reply]

From Algorithm Step 9: "(It is proved that the distribution of Smith-Waterman local alignment scores between two random sequences follows the Gumbel EVD, regardless of whether gaps are allowed in the alignment)."

Can somebody please provide me with a reference for this claim (I mean the second part of the sentence)? To the best of my knowledge, it has never been proven that alignments with gaps also follow a Gumbel distribution. This has only been "proven" empirically by doing lots of computation, and is now somehow "accepted" in the Bioinformatics community. As far as I know, there is not even a closed form to compute the parameters of the Gumbel distribution for alignments with gaps. Since I am teaching courses on Sequence Analysis, I would love to see the paper where they finally close this longstanding open problem. Otherwise (and I believe this is the case) the sentence has to go. —Preceding unsigned comment added by 141.35.12.51 (talk) 09:52, 22 October 2008 (UTC)[reply]

Open source?

I would like to review an algorithm. However there is no obvious source distribution at http://mitc-openbio.sourceforge.net (well hidden may be?) Instead mitrionics proposed to buy it —Preceding unsigned comment added by 85.141.206.213 (talk) 15:42, 11 March 2008 (UTC)[reply]

BLAST IS open source: see ftp://ftp.ncbi.nih.gov/toolbox/ --Plindenbaum (talk) 15:22, 13 March 2008 (UTC)[reply]

Step 3: List the possible matching words.

Would it be fair to say the step 3 is performing a gloabl alignment for each k-letter word from the query sequence against all possible k-letter words? --Rwcitek (talk) 16:28, 4 September 2008 (UTC)[reply]

Most cited reference in the whole of science

Not five minutes ago, by advanced bioinformatics professor told us that the BLAST program was the most cited reference in the whole os science. What do you think ? XApple (talk) 14:06, 23 September 2008 (UTC)[reply]

Yes, a far as I know it is true. Each time the algorithm is cited in a publication the authors are supposed to add a reference of the original paper.--Plindenbaum (talk) 17:34, 23 September 2008 (UTC)[reply]

This is not true. It is only the most cited paper from Journal of Molecular Biology. As far as I know the most quoted paper is still the protein concentration determination method by Lowry. See http://www.jbc.org/content/280/28/e25.full Nicolas Le Novere (talk) 22:20, 29 June 2011 (UTC)[reply]

Algorithmic complexity

I suspect it would probably be good to have some indication of the complexity of the algorithm. If S-W is O(L²) and there are N comparisons then SW would be O(L²N). Is the speed up in Blast on the L2 part or the N part or both? Is there a reference or way to predict the complexity? Pdschloss (talk) 19:35, 13 December 2008 (UTC)[reply]

Since the whole point of FASTA and BLAST is to narrow the range of significant sequences and not perform "useless" matches, N is reduced (following the above formula). Note that for each significant hit a full Smith-Waterman is performed, so no savings on the L2 part there. Jimhsu77479 (talk) 06:43, 6 March 2009 (UTC)[reply]

Two-hit method - Extension

In the page it says that two hits on the same diagonal within a certain distance A is joined together and then extension is performed. This is wrong. Only the second hit is extended, and if the alignment score for this second hit gets above some certain threshold, then a seed is determined (I'll explain how later), and a gapped alignment (DP process) from this seed is triggered both forward and backward.

Relation between eTBLAST and BLAST?

Is eTBLAST an adaptation of the implementation of BLAST for electronic text? Or is just the same underlying idea, but a new implementation? 217.237.64.48 (talk) 16:36, 14 February 2012 (UTC)[reply]

Copyediting

The algorithm has uses of the word "we" which indicate the probable need of copyediting (and that just fixing these occurences of "we" may not be complete.) Does anyone feel they are good at copyediting algorithms or does anyone want to list other items that need polishing? RJFJR (talk) 22:35, 14 February 2012 (UTC)[reply]

PSI-BLAST

...redirects to BLAST, but is given a very cursory treatment. Would it warrant its own page? Ketil (talk) 08:10, 8 August 2012 (UTC)[reply]

Quotes without citations

In the article, two quotes are given ("guarantee the optimal alignments of the query and database sequences" and "ensured the best performance on accuracy and the most precise results"), however, these are not clearly cited. Is this a mistake or an accepted way of giving quotes? Zpon (talk) 09:33, 25 August 2013 (UTC)[reply]

External links modified

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Alternatives to BLAST

The paragraph about KLAST may be commercial speech and it may be out of date. KLAST is hyperlinked to a commercial web site that says the company is defunct. The claim that "Results of KLAST are very similar to BLAST, but KLAST is significantly faster..." requires a technical reference. The text currently has no link to a technical publication and I don't know of any such publication. Jason.Rafe.Miller (talk) 17:41, 29 November 2015 (UTC)[reply]

Disambiguation, biotechnology, protocol

The protocol (and the software implementing it, described in BLAST (protocol)), was up and running in the 1980s. The bioinformatics tool began somewhat later, 1990. Both are oldies, and both deserve respect in referencing.

Both have one or more similar-named relatives: MacBLAST for the protocol, the government-funded BioTech open-source software having PSI-BLAST, eTBLAST and KLAST (all three mentioned above).

The protocol article has no tags/HatNotes; this does.

The protocol article, to which 27 articles link, originated November 2013; the Biotechnology item, to which 48 articles link, originated November 2003. This seems to give the earlier article a possible "primary" status. Per the following Wiki policy guidelines:

following the "Redirecting to a primary topic" Einstein-like suggestion, having BLAST redirect to (biotechnology) does not inconvenience current users of the earlier article;
following the "Primary topic with only one other topic" guideline, a note on top will serve as disambiguation with no need for a formal page. Pi314m (talk) 03:40, 16 July 2019 (UTC)[reply]