Talk:Multiple sequence alignment: Difference between revisions

Revision as of 23:37, 10 September 2006

Latest revision as of 03:02, 5 April 2025

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{{ArticleHistory

{{GAnominee|3 September 2006}}

|action1=GAN

|action1date=04:03, 12 September 2012

|action1result=listed

|action1oldid=75224080

|action2=GAR

== Good article nomination ==

|action2date=18:51, 7 March 2010 (UTC)

|action2link=Talk:Multiple sequence alignment/GA1

|action2result=kept

|action2oldid=348064247

|topic=Natsci

My suggestions:

* in section Dynamic programming and computational complexity + Progressive alignment construction (after finishing the article, I must say in nearly all sections), there are several external links that should be converted into internal references

* <s>Maybe not so important, but a reference for that statement: "PRRP performs best when refining an alignment previously constructed by a faster method." would be useful</s>

* "which is also available as a web portal": this kind of sentences should be all converted into reference. It looks bad in the article.

* What about external links section? I now the article is full of external links (see above), but there must be some links writing about MSA.

Anyway, absolutely great article, I'm not an expert in that topic, but I could easily read it. Congrat! [[User:NCurse|NCurse]] _{[[User talk:NCurse|work]]} 07:03, 10 September 2006 (UTC)

: Thanks. I'm glad it's readable by a knowledgeable non-expert; bioinformatics can be very difficult to explain well. I agree that not all the external links are written/segued into very well, but integrating them into the text was a (semi-)conscious decision also followed in the parent [[sequence alignment]] and the (siblings, I guess?) [[structural alignment]] and [[computational phylogenetics]]. I figure that many readers are probably looking for a way to actually perform a sequence alignment, and if they find a method they like, it's much easier to have the external link in the relevant paragraph than at the bottom of the article. Tracking down the current download page/web portal from the original paper can also be a challenge, since these things change hosting/get absorbed by larger projects/follow a postdoc when he sets up his own lab/etc. On rereading I do notice a couple of programs that have an external link but no literature reference, so I'll clean that up.

|action3 = GAR

: The PRPP statement belongs to ref #9, which appears in the immediately preceding sentence as well. I added a second note - do you think that looks redundant? I'll look for useful links tomorrow - there's lots of them but the signal-to-noise ratio is not so great. [[User:Opabinia regalis|Opabinia regalis]] 07:57, 10 September 2006 (UTC)

|action3date = 16:58, 11 April 2024 (UTC)

|action3link = Wikipedia:Good article reassessment/Multiple sequence alignment/1

|action3result = delisted

|action3oldid = 1217842964

|currentstatus = DGA

}}

{{WikiProject banner shell|class=B|1=

{{WikiProject Molecular Biology|importance=High|genetics=yes|genetics-importance=mid|MCB=yes|MCB-importance=mid|COMPBIO=yes|COMPBIO-importance=high

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==some clarifications==

:: FYI, I added external links and references to the tools that were paperless, and cleaned up some of the web portal links. I did leave the direct external links to the relevant tools, but hopefully a bit more integrated. What do you think? [[User:Opabinia regalis|Opabinia regalis]] 23:37, 10 September 2006 (UTC)

the statement

<div style="border:1px solid black;padding:5px;">

Because HMMs are probabilistic, they do not produce the same solution every time they are run on the same dataset; thus they cannot be guaranteed to converge to an optimal alignment. HMMs can produce both global and local alignments. Although HMM-based methods have been developed relatively recently, they offer significant improvements in computational speed, especially for sequences that contain overlapping regions.

</div>

is incorrect. HMMs are probablistic in the sense that they are a statistical model, however, they are completely deterministic and will produce the same result every time on a given dataset. HMM alignments use the same algorithms as local sequence alignments and therefore have no computational speed advantage.

<div style="border:1px solid black;padding:5px;">One of the most common motif-finding tools, known as MEME, uses expectation maximization and hidden Markov methods to generate motifs that are then used as search tools by its companion MAST in the combined suite MEME/MAST.[19][20]

</div>

MEME uses a PSSM (position specific scoring matrix), but does not contain insertion or deletion probabilities or other characteristics of a typical sequence HMM.

[[User:Gribskov|Gribskov]] 03:55, 20 September 2007 (UTC)

== [[Short-read sequence alignment]] ==

Given the specific technological and algorithmic and biological significance of [[short-read sequence alignment]], I think this topic deserves its own page. For example, the differences between short read mapping and de-novo assembly in [[next-generation sequencing]] projects could be discussed on such a page. --[[User:dmb000006|Dan]]|^{[[User_talk:Dmb000006|(talk)]]} 14:01, 22 January 2009 (UTC)

== Alternative interpretations of MSAs ==

The main use/interpretation of columns in MSAs is that residues in the same column are "related" by either point substitutions or no substitutions at all.

However, there are applications of MSAs where residues in the same column are assumed to be "structurally" equivalent but not necessarily evolutionarily equivalent e.g. http://www.ncbi.nlm.nih.gov/pubmed/16733545 - indeed in some of these applications the aim is to avoid including "homologous" sequences in the alignment e.g. http://www.ncbi.nlm.nih.gov/pubmed/9920390

At the moment this distinction isn't made on the MSA wikipedia page - although the top of the [[sequence alignment]] wikipedia page does highlight different interpretations.

First wikipedia post ever here - not quite ready to be bold yet! - so wanted to ask/check whether anyone disagrees with introducing some changes to reflect this distinction to the MSA page?

[[User:SiggyDood|SiggyDood]] ([[User talk:SiggyDood|talk]]) 12:45, 11 March 2009 (UTC)

{{/GA1}}

== External links modified (February 2018) ==

Hello fellow Wikipedians,

I have just modified 4 external links on [[Multiple sequence alignment]]. Please take a moment to review [[special:diff/824573909|my edit]]. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit [[User:Cyberpower678/FaQs#InternetArchiveBot|this simple FaQ]] for additional information. I made the following changes:

*Added archive https://web.archive.org/web/20100311140200/http://www.ebi.ac.uk/help/matrix.html to http://www.ebi.ac.uk/help/matrix.html

*Added archive https://web.archive.org/web/20060705082556/http://align.genome.jp/ to http://align.genome.jp/

*Added archive https://web.archive.org/web/20060909003117/http://pbil.univ-lyon1.fr/alignment.html to http://pbil.univ-lyon1.fr/alignment.html

*Added archive https://web.archive.org/web/20090821192233/http://bioinf.may.ie/school02/notes.html to http://bioinf.may.ie/school02/notes.html

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==GA Reassessment==

{{Wikipedia:Good article reassessment/Multiple sequence alignment/1}}