User:WeepingBritney/Sequence alignment prof review

Breadth

 * Does the article cover its field completely?

The article touches upon most of the relevant aspects although some parts are covered much more extensively than others. Some aspects are not described in sufficient detail (see below).


 * Are all the common terms of the field defined?

Most terms are defined in the article or can be understood by following links to other Wikipedia pages, but the article tends to use more jargon than necessary.


 * Are all the basic concepts of the field described?

Yes for the most part, but not very clearly, especially not for students learning this material for the first time.


 * Were important topics missed?

The article does not describe combined sequence/secondary structure alignments which is common in alignment methods that specialize on remote homologs where simple sequence alignments are not successful. The article is not very clear on profile-based sequence alignment methods. Furthermore, it neglects to discuss consensus alignment servers that have become popular in the recent past.

Depth

 * Amount of detail appropriate for topic

I would say the amount of detail depends on the target audience rather than the topic. The amount of detail is probably not enough for a student learning the material for the first time. It is also too superficial for a researcher familiar with a related area to gain a good understanding of the area.


 * History given?

Not really.

Readability/Writing

 * Is the writing clear?

I find the writing stylistically appropriate but somewhat dense.


 * Is the writing interesting?

That depends on the reader, but I found the text fairly dry.


 * Is the writing organized, good flow?

There is room for improvement. Often sentences only really make sense with explanations given further down in a given paragraph.


 * Architecture of the article

The organization of the material is somewhat scattered. It would make much more sense, e.g., to discuss scoring matrices near the beginning of the article.


 * Is the writing redundant?

For the most part not.

Learnability

 * Is the level of explanation good for undergraduate students?

The article, by itself, is probably not adequate for most students. It assumes fairly extensive knowledge about bioinformatics, structural biology, and certain computational methods. However, a diligent student could probably learn enough from following Wikipedia links to understand most of the article.


 * Is the teaching well-organized?

As mentioned above, the organization is somewhat scattered and probably not helpful in clearly explaining the subject to the reader.

Figures

 * Are there Figures at all?

Yes.


 * Are the Figures clear?

Yes.


 * Are the Figures three-dimensional?

No.


 * Are the Figures consistent with each other?

Yes.


 * (my question): Should there be more figures?

Yes. Additional figures would greatly enhance the readability of the article. E.g. one could illustrate sequence vs. structural alignment.

Quality

 * How up-to-date is the article?

The article is mostly current. It might be out of date by a few years in some aspects because it does not cover combined sequence/secondary structure based methods and consensus methods.


 * Glaring errors, minor errors, and misleading statements?

I did not find glaring errors but there are some sentences that do not seem to make much sense such as "Although DNA and RNA nucleotide bases are more similar to each other than to amino acids ..."


 * How precise and quantitative is this article?

Not much. It describes sequence alignment on a technically dense but fairly high level. It could be much more specific with respect to different methods.