CBMDB: A Database for Accessing, Analyzing, and Mining CBM Information
Round 1
Reviewer 1 Report
The work of Lin et al. entitled "CBMDB, A Database for Accessing, Analysis and Mining CBM Information" has as a proposal the implementation of a database of CBMs. The contribution of the work is to provide online bioinformatic tools that allow sequence analysis for the identification of CBMs. Which does not exist in the CAZY database, which is also a repository of CBMs information, but which lacks the bioinformatics tools that allow further analysis.
Minor comments
Line 11: Define CBM.
Line 33: Suggestion. Put a period at the end of "identified and characterized, the total ..." so that it looks like this "identified and characterized. The total ..."
Line 148: Missing a comma in the number 533496.
Line 149; Missing a comma in the number 143015.
Line 150: Missing a comma in the number 143316.
Major comments
1.- More information on the applications of CBM in the context of enzyme engineering is needed in the introduction, so that the biotechnological importance is clearly understood.
2.- As well as on the molecular mechanism through which CBMs act, what do they do? how do they do that?, etc.
3.- Section 2.3 and 2.4 have the same title. Why?
4.- Data query with a sequence gives no results found. This is one of the sequences I tried:
>AAC44232.1 beta-1,4-mannanase [Caldicellulosiruptor saccharolyticus]
MGVCLDMWRNWRVLFVLVTIIFLFSLIPTGIFGAVESSVNPVVLDFEDGTVMSFGEAWGDSLKCIKKVSV SQDLQRPGNKYALRLDVEFNPNNGWDQGDLGTWFGGVVEGQFDFTGYKSVEFEMFIPYDEFSKSQGGFPY KVVINDGWKELGSEFNITANAGKKVKINGKDYTVIHKAFAIPEDFRTKKRAQLVFQFAGQNSNYKGPIYL DNVRIRPEDASNLSKEDYGEQAEEGVAVEDFFTGVKLVYPEQGKSFVYNFEIDTMGFYKYSGDGFNKKTK SLEYSQDLKRSGNNGALKVNASLAGTAFDEMNIAIKLTDKDDKKFDFSKYSTLEYTLYIPNPDKISGKLM VASAIDNPWQIIKDFTAINYKDKNAIQKINGKDYAVIKCSDNLYNVNTKANVLVLRIAGSYVKYTGPIYI DNVKLVAGKKVAPKVKTTSSIPNIKNYYRVKIEAETAKDGWAYSIEKENAKYSGKGYILLFGNNMGNTLY DLKIPKTGYYIFTISSSTLGMVNYGSVDIWIDGELKGAAKVPNVKGKFQEVVVMKKIYLTQGEHTLSLQK SGGYTIAIDYFTIEELVLANKNKISVDTKLVTPNPHPNAQKLMKYLASIYGEKILSGQQSSGDGKEIQMI FDVTKRYPAVRGFDFMDYSPSRVEHGTKGTDVEEAIKWWKSGGIVAFCWHWNAPTGLIDQPGKEWWRGFY TEATTFDIKKAMDNPNSTEYKLILRDIDAIAEQLKRLQKEGVPVLFRPLHEASGGWFWWGAKGPEPYIKL WKLMFDRLVNYHKLNNLIWVWNGQDAAWYPGDNYVDIIGEDIYEEKAQYSPYADRFAKALKYTNARKMIA LTECGTIPDPAVLKQEGISWSWFSVWAGNFVMTGSKYNDEWNDNHMLRKIYNSDYVITKDELPDIKNIPL
5.-The structure similarity search tool does not work. I tried with an aa sequence and it gives an internal server error 500.
6. Authors should implement other sequence analysis tools such as weight-position matrices or hidden Markov models.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
First of all congratulations to the authors for the article. The article is very good and describes a very interesting tool. The only weak point is in the lack of information about other similar tools and the unique contribution of the presented tool. The process of extraction and homogenization of the information obtained is also a bit short, since as it is described, it is implied that there is a parser made directly for each source. The images are very out of place and too close together, especially image 2 and 3, which are practically next to each other and with the letters repeated to separate each image in image 3. They should be redistributed more continuously throughout the document. Regarding the publication of the article, it is subject to the contribution that can be demonstrated against similar tools, where if there is a clear contribution, it will be a pleasure to consider it ready for publication.Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Reviewer 3 Report
The paper describes a system resulting from the integration of several data and tools available on the Internet.
The application area - the mechanism of enzyme-carbohydrate recognition and the process of enzymatic engineering - is important to researchers and the architecture of the system is reasonable,
However, the figures 2, 3, and 4 cannot be read and should be enlarged and inserted near the text referring to it.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
With the improvements applied to the article, the problems that could be observed in it have already been solved. Therefore I recommend your publication.