Wikipedia:Featured article review/Sequence alignment/archive1


 * The following is an archived discussion of a featured article review. Please do not modify it. Further comments should be made on the article's talk page or at Wikipedia talk:Featured article review). No further edits should be made to this page.

The article was removed by YellowAssessmentMonkey 00:47, 1 September 2009.

Review commentary

 * Notified: Opabinia regalis, WikiProject Molecular and Cellular Biology

I am nominating this featured article for review because of 1c concerns. The article has been edited extensively since it passed FAC in July 2006 and there are whole sections that are unreferenced. It has been tagged for  &mdash; Mattisse  (Talk) 00:56, 2 August 2009 (UTC) "Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. Calculating a global alignment is a form of global optimization that 'forces' the alignment to span the entire length of all query sequences. By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. A variety of computational algorithms have been applied to the sequence alignment problem, including slow but formally optimizing methods like dynamic programming, and efficient, but not as thorough heuristic algorithms or probabilistic methods designed for large-scale database search." &mdash; Mattisse (Talk) 18:58, 2 August 2009 (UTC)
 * The lead is only two sentences on a complex subject, violating WP:LEAD.
 * The lack of citations suggest the much of the article may be original research. For example, this uncited section:
 * Images need alt text as per WP:ALT. Eubulides (talk) 06:03, 2 August 2009 (UTC)
 * Hmm. I haven't decided yet whether I'm going to have the time to update this article, but I'm really glad to see that alt text has been implemented. Still, I'm at a loss as to how to write useful alt text for a sequence alignment... I mean, it already is text; the trick is in the formatting. Since you seem to be the alt-text expert, do you have any suggestions? Perhaps at least one alignment can be presented as text in table format rather than as an image? I think that would help text-based browser users, but I'm not sure about screen readers. Thoughts? Opabinia regalis (talk) 19:52, 2 August 2009 (UTC)
 * You're right to be cautious about screen readers: they do tables, but sometimes it's easier to summarize the gist of a table in text rather than to list each row and column separately. However, for the two sequence-alignment images here I expect that tables would be better. Even for a sighted reader a table can be better, e.g., you can copy and paste from it. Eubulides (talk) 20:33, 3 August 2009 (UTC)


 * General comment I agree that this article is in need of an update, though I'm not sure yet that I'm going to have the time to do it. "Citing" it is a bit of a red herring; references to a bioinformatics textbook would technically be appropriate, although I'd rather also include the references to the original descriptions of the older methods (even if the 'standard' current implementation has been modified from the original). For one thing, the prose has degraded (not that mine was brilliant to begin with). And three years is a long time; there are new methods that belong here (relatedness-aware MSA methods should certainly be included) and dead links to prune (the software subarticle looks like the lawn of a home in foreclosure). Lastly, it's suffering from the bias of its author in that most of the examples derive from protein rather than nucleic acid sequences, and there's very little on methods used in genomics. (As a side note, I'm really surprised to find things like PSI-BLAST not even mentioned by name.) Opabinia regalis (talk) 20:07, 2 August 2009 (UTC)
 * Sorry, it's not looking good for finding the time to fully update this; I'm in the middle of revisions for a real paper. Sounds like the best way to show an alignment is either a table or a preformatted text box, although I'd like to keep at least one image showing a large MSA (perhaps not the current one, which is a screenshot from software that was rather old 3 years ago). I'll try to at least update the images and insert the original refs for the methods next week, though that won't help with the dated text. Opabinia regalis (talk) 03:17, 16 August 2009 (UTC)

FARC commentary

 * Suggested FA criteria concern are citations, alt text. Also note the recent change to WP:WIAFA (1c) requiring "high-quality" sources. FAQ?  YellowMonkey  ( cricket photo poll! '') paid editing=POV 01:55, 17 August 2009 (UTC)


 * Delist per the concerns of Opabinia regalis. The article needs an expert in the subject. JKBrooks85 (talk) 06:49, 17 August 2009 (UTC)
 * Delist per above and per nom. &mdash; Mattisse  (Talk) 14:33, 17 August 2009 (UTC)
 * Delist If Opabinia agrees that the article needs significant work, then it probably does. There's not much that can be done here without an expert. Better to delist and have it resubmitted when it's up to standard again. Dabomb87 (talk) 15:01, 17 August 2009 (UTC)
 * Delist, per FA criteria concerns, and above comments. Cirt (talk) 06:12, 26 August 2009 (UTC)
 * The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.