Made use of term CR_1.0/rheMac3 (as in UCSC browser). Authors' response: We agree with Dr. Yi that we must always notice that CR_1.0 is termed rheMac3 during the UCSC genome browser and have now completed so from the textual content. However, this is a little bit of a controversial problem as only the unique submitter of the assembly is technically allowed to concern updates. Baylor may need to update their assembly, rheMac2, and would typically consult with their update as rheMac3. Due to the fact BGI has termed their assemblyrheMac3, there may be some confusion if/when Baylor attempts to name their next update. We named our assembly MacaM to prevent contributing to this confusion. p.5/Table 1: I might recognize extra specifics around the logic fundamental the proposed new chromosome nomenclature. Authors' reaction: Chimpanzees, gorillas, and orangutans possess the exact same basic chromosomal structure as humans, with just one notable exception. The human chromosome two seems to be the result of a fusion occasion that happened for the duration of hominid evolution. Thus, the great apes and rhesus macaques each have two chromosomes that about correspond on the limited and extensive arms of human chromosome two. While in the excellent apes, both of these chromosomes are often called 2a and 2b. We adopted the exact same nomenclature for rhesus macaques to generate comparisons concerning various primates less difficult. We've got added extra textual content to our manuscript PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/12711626 to produce this place additional evidently. Incorporating chromosome nomenclature in other ape species may well support the visitors to find out the advantage in the proposed nomenclature system. Authors' response: We now have extra chimpanzee, gorilla and orangutan to Table 1 as requested. p.6 figuring out orthologs of human genes: as explained currently it is not distinct if the reciprocal-best-blast hit strategy is applied; the reciprocal phase employing human reference proteins towards the rhesus macaque transcripts will not be specified. Authors' response: We did not make use of a reciprocal-bestblast strike strategy to establish orthologs of human genes. Also the cutoff values must be provided (e.g. e-value coverage similarity criteria). Authors' response: Just one set of cutoff values wasn't applied mainly because several types of genes evolve at different costs. Our rationale for this is just like that used to decide irrespective of whether sim4cc and GMAP PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/3021955 gene designs were being accurate. We now have added text on the manuscript to produce this clearer. p.7 p.9 conversations on protein sequence annotation and exon misassembly: The authors utilize the illustration on the Src homology 2 area containing E (SHE) gene to exhibit the utility of MacaM assembly and how various annotations differ in their attributes. On the other hand I failed to locate a mention of this gene till this distinct section. It will be awesome to determine why this certain case in point has long been selected. Authors' response: We agree that our dialogue on the misassembly with the SHE gene begins a tiny bit abruptly. We picked this gene for the reason that we had beforehand recognized it as misassembled in an additional paper [3]. We've additional text to the Protein Comparison section of the Approaches to create this obvious. Did they complete Letrozole a worldwide comparison amongst MacaM compared to rheMac2? If they did it'll be good toZimin et al. Biology Immediate 2014, 9:twenty http://www.biologydirect.com/content/9/1/Page 13 ofsee a desk of these effects (further than the Desk 5 which basically implies identity/similarity/gaps) one thing such as mismatch of exon numbers and so on might be beneficial) in addition to the list of curated/improved gene sets. While this is often an optional comment I think that in-depth d.