Review History


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Summary

  • The initial submission of this article was received on December 2nd, 2015 and was peer-reviewed by 2 reviewers and the Academic Editor.
  • The Academic Editor made their initial decision on December 28th, 2015.
  • The first revision was submitted on January 11th, 2016 and was reviewed by the Academic Editor.
  • The article was Accepted by the Academic Editor on January 17th, 2016.

Version 0.2 (accepted)

· · Academic Editor

Accept

The revised version has addressed most of the relevant comments.

Version 0.1 (original submission)

· · Academic Editor

Major Revisions

The review reports are rather critical. Among others, it is required that the authors must be able to justify the validity of the database content.

·

Basic reporting

The abstract looks concise to me.

I cannot find any figure or table for the manuscript. It would be best if the authors could include some figures and tables for user-friendly explanation. It is important as the manuscript is a database paper.

Experimental design

The experimental setting "pattern 12A allowing for one mismatch" has to be carefully supported on the manuscript. Have the authors tried other experimental setting since this setting can significantly affect the database content ?

Validity of the findings

The sentence "Given that no genomic database reports polyA tracks in coding sequences" may be arguable, please look at the following databases and state your difference to them:
http://exon.umdnj.edu/polya_db/
http://bioinfolab.miamioh.edu/polya/
http://mosas.sysu.edu.cn/utr/
https://www.google.com/webhp?q=polya%20database

Comments for the author

It is very nice that the authors have released the scripts which can recreate the
database from the scratch on user's own computer.

The sentence "...is of course a bit simplistic...." is not appropriate on a scientific manuscript.

The first studies
The past studies

gathered researchers' attention
drew researchers' attention

Reviewer 2 ·

Basic reporting

The paper reports generation of a database of coding region polyA sequences from 250 genomes and web service to look this up.
While databases are useful for researchers to look things up in their studies, I am not sure this justifies a scientific report as there is not much experiments or science in this report.
There was also no mention of the validation of the search results at all:should we just trust that the results by the processes reported are reliable? Are all the sequences reported in coding regions? without sequencing errors? I think it is troubling that there is no mentioning of quality examination of the results.

Experimental design

The paper reported the process of collecting the polyA sequences in coding regions. There was no mention of validity check of the results and quality control.

Validity of the findings

No way to judge.

Comments for the author

It is essential to validate the results in the database. It is also important to survey the distribution of such sequences in a few model genomes.

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