ConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design
Round 1
Reviewer 1 Report
1. Content and tool design is new but the content presented needs some changes to make the paper sound .
2. I suggest to check the English Grammar throughout the content by yourself or use the Grammarly tool.
3. You need to write the definition and history of DNA in simple language. Kindly separate the paragraphs or segregate the content into simple definitions, history, and requirements. Some related or previous tool used for this need to be added in the existing literature.
4. Add references to support the content.
5. Comparision with other pipeline techniques are missing.
Comments for author File: 
Comments.pdf
Author Response
Point 1: Content and tool design is new but the content presented needs some changes to make the paper sound.
The paper was revised to improve comprehensibility. In addition, the flowchart was updated.
Point 2: I suggest to check the English Grammar throughout the content by yourself or use the Grammarly tool.
The English grammar was revised using the Grammarly tool.
Point 3: You need to write the definition and history of DNA in simple language. Kindly separate the paragraphs or segregate the content into simple definitions, history, and requirements. Some related or previous tool used for this need to be added in the existing literature.
The introduction has been extended by a brief definition of DNA.
Point 4: Add references to support the content.
Further references have been added.
Point 5: Comparison with other pipeline techniques are missing.
The reasoning behind avoiding any pipelining techniques, such as, snakemake or nextflow has been included.
Regarding the comments from within the submitted Document:
Comment M1-M5, M8, M13
These comments have been addressed already with the points above.
Comment M6
The flow chart has been updated to better show how the individual modules are linked. The basic model of oligonucleotide DNA hybridizations is based on Wats-Crick base pairing and the formation of hydrogen bonds between A and T (2) and G and C (3). This is also the basis for all modules and combined software units and calculations used.
Comment M7
There standard version of Mafft is used. The citation has been changed to avoid ambiguity.
Comment M9
The figure title has been shortened.
Comment M10
The relevant part has been moved to the Methods section.
Comment M11
The figure title has been shortened.
Comment M12
The relevant part has been moved to the Methods section.
Reviewer 2 Report
Manual identification of suitable consensus regions and alignment of sequences is impractical specially for large and inhomogeneous alignments. This work reports a pipeline for automatic detection of optimal consensus regions for large alignments with many sequences. The introduction is precisely described. However, the reviewer recommends resolving the following issues:
1. Prime pipeline was developed sort out-> Prime pipeline was developed to sort out
2.The title of the figures must be separated from the paragraph
3.Figure 2 must be updated using the typical flowchart symbols. Finding the star point and comprehending how the process works are challenging.
4. Information regarding Ethics Committee or Institutional Review Board approval should be included. If not, the authors should include the explanation.
Author Response
Point 1: Prime pipeline was developed sort out-> Prime pipeline was developed to sort out
Changed as requested.
Point 2: The title of the figures must be separated from the paragraph
The title was separated and the paragraphs have been reworked and moved to the Methods section as suggested by Reviewer 1.
Point 3: Figure 2 must be updated using the typical flowchart symbols. Finding the star point and comprehending how the process works are challenging.
The flowchart has been reworked for a more streamlined depiction and with updated symbols.
Point 4: Information regarding Ethics Committee or Institutional Review Board approval should be included. If not, the authors should include the explanation.
An Ethics Committee is responsible for the ethical and legal assessment of research projects involving human subjects (including deceased subjects) and extracted body material, for epidemiological research projects involving personal data, for experiments involving animals or for experiments on dangerous pathogens as well as for advising responsible researchers. Therefore, in our present work, which deals with software, this is neither applicable nor necessary.
