Talk:Sequence Search and Multiple Sequence Alignment (PKU)

This is just a place to add criticism and or positive feedback so we Jonathan and Sebastian have a possibility to improve. Please note, that we wont be able to adress all matters immediately but we will address them eventually!

source: [1]

criticism

• Despite some offline discussion I still do not get this sentence:

In order to display the runtime PSIBlast uses in order to get results you asked for we used a little skript which uses PSIblast with a variety of parametersettings. (Section 3.2 PSIBlast) --Rackersederj 19:47, 7 May 2012 (UTC)

• • it makes perfect sense to me --Hollizeck 20:18, 7 May 2012 (UTC)

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In the section evalues there are two references to table 2 where the second one should point to table 3. Staniewski 22:24, 7 May 2012 (UTC)

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It's not always clear to me which settings were used in the Psi-Blast section. For example in section evalues:

• How many iterations did you configure for the results of the first picture set?
• What e-Value cut-offs were used for the second picture set?

Did you only adjust the iterations OR the e-value cut-off or did you also change these two options at the same time? Staniewski 22:24, 7 May 2012 (UTC)

MSA

You generated your datasets for the msa analysis from the blast result you describe in the PDB paragraph above, right? Or are you talking about another "big80 search" here? Staniewski 22:30, 7 May 2012 (UTC)

positive feedback

• I really liked the way you explain why you did use some specific methods or tools (e.g. why you used GO term comparison .. "After analyzing the output of each of those tools through standard numeric methods we wanted to see if one can see a quality difference with something more concrete than e-Values and identities")

--Rackersederj 20:03, 7 May 2012 (UTC)

suggestions

Just a formal suggestion: The section 'Database Searches' is quite hard to read since there are several newlines missing, especially in the e-Vales subsection. You could put these parts in 'preformatted text' boxes for example. Also, your figure 1 does not exist (yet?). Staniewski 10:04, 7 May 2012 (UTC)

The section is still work in progress, but your points have mostly been fixed, thanks! Boidolj 13:12, 7 May 2012 (UTC)

• In Figure 1 I would suggest another set of colors, since red, blue and purple are a little hard to distinguish here. --Rackersederj 19:50, 7 May 2012 (UTC)
• It is a little confusing if you refer to a table if you actually mean a set of figures. You might want to try using "gallery" --Rackersederj 19:57, 7 May 2012 (UTC)

The "Table X" part is generated by mediawiki, but I agree, it's a little bit confusing. Maybe you can find a way to label the tables at least. I had to click on the link until I realized that 'Table 8' was referring to the three pictures above the sentence. ;) Staniewski 21:55, 7 May 2012 (UTC)