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{{Wikiproject MCB|class=GA|importance=mid}}
== Good article nomination ==
My suggestions:
* <s>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>
* <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>
* <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.</s>
* <s>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.</s>
Anyway, absolutely great article, I'm not an expert in that topic, but I could easily read it. Congrat! [[User:NCurse|NCurse]] <sub> [[User talk:NCurse|work]]</sub> 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.
: 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)
:: 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)
Some things left:
* <s>"A web portal and download site is available at MUSCLE."
* "A database-search technique based on HMM methods is available in the program HMMer.[14]"
* "A server for locating motifs in unaligned sequences is located at BLOCKS.".....etc
I think the external links (not internal references) can stay in the article, but they should be merged into the paragraphs, because now these are lonely statements.</s> Anyway everything seems to be good to me. [[User:NCurse|NCurse]] <sub> [[User talk:NCurse|work]]</sub> 13:12, 11 September 2006 (UTC)
: I think I got them all, thanks. [[User:Opabinia regalis|Opabinia regalis]] 04:06, 12 September 2006 (UTC)
Great work, thanks for the reactions. Congrat! :) It's now a [[WP:GA|good article]]. [[User:NCurse|NCurse]] <sub> [[User talk:NCurse|work]]</sub> 14:47, 12 September 2006 (UTC)
: Thanks for the review! [[User:Opabinia regalis|Opabinia regalis]] 01:03, 13 September 2006 (UTC)
==some clarifications==
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