Minor Essential Revisions:

The descriptions for TBLASTN and TBLASTX need to be swapped in Table 1 (rows 4 and 5).

Discretionary Revisions

This is a well structured and informative article about supporting sequence similarity searching (BLAST) in Galaxy. The Results section contains a number of example applications such as "Assessing a de novo assembly". This section does have references to some of the tools that would be useful in this task (e.g., seq_filter_by_id), but I find these examples somewhat abstract. Additionally, a reader unfamiliar with Galaxy might not be convinced of the advantages of using Galaxy for these tasks as opposed to simply running the searches themselves. I'd suggest that the authors add a concrete example of one of their use-cases. For example, the authors could show how their tools could find the globin cluster for some mammal. This should include all accessions and other information so that a reader could reproduce the result. This example could be added as supplementary material if need be. Level of interest An article of importance in its field Quality of written English Acceptable Statistical review No, the manuscript does not need to be seen by a statistician. Declaration of competing interests I declare that I have no competing interests.

Authors' response to reviewers: (http://www.gigasciencejournal.com/imedia/2914911191674395_comment.pdf)