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khmer version & citation clarification (Michael Crusoe, 23 November 2015)

There is no version 0.2 of khmer; we suspect that the authors used version 2.0, as that matches their citation. We appreciate the citation of our software though we request that both the software and the matching algorithm paper be... read full comment

Comment on: Hara et al. BMC Genomics, 16:977

Our prediction of the relationship between Tingal1 and metastasis was validated. (Y-h. Taguchi, 17 November 2015)

Dear Readers,  I am the corresponding author of this paper. Recently, our prediction  of the relationship between Tingal1 and metastasis was validated indirectly, but experimentally.  Takahashi et al [1] reported that Tingal1 plays potential roles for fertility. The authors suggestd that our findings of the relationship bwteen metastasi and Tingal1 indirectlty supprted their findings. For more details, read their paper. Yours, tag [1] Takahashi et al, Impaired female fertility in tubulointerstitial antigen-like 1-deficient mice, J Reprod Dev. (2015)  [Epub ahead of print] read full comment

Comment on: Umeyama et al. BMC Genomics, 15:S2

Formatting mistake in Table 1. (Lua Perez, 09 November 2015)

The content of the first row in Table 1 is incorrectly placed to the left side of the table. Each category in that row should cover two columns of the table. That means that, genomic should cover the first two columns for Oryza and Arabidopsis, Intron the next two Oryza and Arabidopsis and so on. read full comment

Comment on: Lopez et al. BMC Genomics, 16:781

Alternative explanation for low levels of synteny observed in the strawberry genome (Aaron Liston, 02 November 2015)

The relatively low synteny with the strawberry genome (Fv) would likely disappear using the improved assembly of the Fragaria vesca genome (Tennessen et al 2014) The new assembly can be downloaded from read full comment

Comment on: Luo et al. BMC Genomics, 16:707

Strawberry synteny (Aaron Liston, 08 October 2015)

The unexpected lack of synteny with the strawberry genome would likely disappear if the most recent assembly of the Fragaria vesca genome was used (Tennessen et al 2014). Their new assembly has much greater synteny to the peach genome: The new assembly can be downloaded from     read full comment

Comment on: Staton et al. BMC Genomics, 16:744

Mistakes in the equations. (Luay Nakhleh, 05 October 2015)

We apologize that we made a few minor mistakes in the equations. The fixes are minor and the results would still hold with these... read full comment

Comment on: Yu et al. BMC Genomics, 16:S10

List of authors (Peter Kamp Busk, 02 October 2015)

I was mistakenly omitted from the author list. I developed a new method for data mining (PPR) and used it for the peptide pattern analysis. The listed authors have been most helpful in correcting this. They were told by BMC Genomics that it was too late to change the official author list but they were welcome to submit a comment to the paper. Hence, they submitted a statement about my contribution to the paper to BMC Genomics more than a year ago but it has not been listed by the journal. read full comment

Comment on: Grell et al. BMC Genomics, 14:928

cisPatterns (Jermaine Ross, 30 September 2015)

Be sure to visit! read full comment

Comment on: Ross et al. BMC Genomics, 16:700

About author's contribution (Nasheeman Ashraf, 18 September 2015)

Shoib Ahmad Baba and Tabasum Mohiuddin contributed equally and are first authors. Swaraj Basu and Mohit Kumar Swarnkar contributed equally and are second authors. read full comment

Comment on: Baba et al. BMC Genomics, 16:698

Acknowledgements (Viviana Echenique, 07 September 2015)

We acknowledge Dr Norma Paniego (Instituto de Biotecnología, INTA, Argentina) and Ing Bernardo Clavijo (The Genome Analysis Center, UK),  for contributing the 454 read assembly used in this work. read full comment

Comment on: Garbus et al. BMC Genomics, 16:375

Founder mutation in EYS (Akio Oishi, 18 August 2015)

I read with interest the article by Yoon et al. They are to be congratulated for demonstrating the genetic overview of Korean RP... read full comment

Comment on: Yoon et al. BMC Genomics, 16:515

Data availability BioProject PRJNA244102 (Brieanne Vaillancourt, 06 August 2015)

During the proof stage, the NCBI SRA project number was accidentally omitted. Reads have been deposited in the National Center for Biotechnology Information Sequence Read Archive under BioProject PRJNA244102 read full comment

Comment on: Zuluaga et al. BMC Genomics, 16:246

Correction typing error species name: Tydemania expeditionis (Frederik Leliaert, 06 August 2015)

There was an unfortunate typing error in the species name of Tydemania. The correct spelling is "Tydemania expeditionis", and not "Tydemania expeditiones". read full comment

Comment on: Leliaert et al. BMC Genomics, 16:204

Update: Corrected SRA accession number and Dryad DOI. (Rachel Wright, 09 July 2015)

"“R scripts and input files can be accessed on Dryad: doi:10.5061/dryad.8mr56. Raw sequence data can be found on NCBI-SRA, Accession: SRP057962."
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Comment on: Wright et al. BMC Genomics, 16:371

Acknowledgement (Travis O'Brien, 08 July 2015)

The authors thank Ms. Mamta Giri for assistance creating the circos plot read full comment

Comment on: Orkunoglu-Suer et al. BMC Genomics, 16:264

YgjD - YeaZ - YjeE protein-protein interactions (Peter Uetz, 25 June 2015)

As an example (and control) of how the ORFs of this study can be used to study protein-protein interactions, we somewhat arbitrarily selected 3 proteins: YgjD, YeaZ, YjeE, which had been purified in a complex before. Unfortunately, this was not mentioned in the abstract. However, these interactions turn out to be quite interesting and several groups have studied them independently. Most recenlty, Zhang et al. presented crystal structures of YgjD–YeaZ–YjeE from E. coli and their interactions in read full comment

Comment on: Rajagopala et al. BMC Genomics, 11:470

New web address (Jizu Zhi, 11 June 2015)

The application has been moved to   read full comment

Comment on: Zhi et al. BMC Genomics, 9:407

Updated Rubber Genome Browser URL (Jennifer Saito, 23 April 2015)

The URL listed in reference #90 has been changed.  Please use the following link to access the Rubber Genome Browser: read full comment

Comment on: Rahman et al. BMC Genomics, 14:75

Correction to the Funding Agency and project under the Acknowledgements section  (Cecilia Jimenez-Mallebrera, 23 March 2015)

This work is funded by the " Plan Nacional de I+D+I and Instituto de Salud Carlos III– Subdirección General de Evaluación y Fomento de la Investigación Sanitaria", project PI10/00177,  and the European Regional Development Fund (FEDER).  read full comment

Comment on: Kalko et al. BMC Genomics, 15:91

Correction to figure 4 and the text associated is still in the production process (Youxiong Que, 09 March 2015)

Following the publication of this article, it came to our attention that we neglected to acknowledge the inspiration for figure 4 and the text associated with the figure 1 provided by Bakkeren and colleagues read full comment

Comment on: Que et al. BMC Genomics, 15:996

Inversion of two additional files (Muriel GUGGER, 05 March 2015)

The links of the additional files 1 and 2 have been inversed. Thus, the additional file 1 which should be containing the Tables S1, S2, S3 and S4 into a 76 KB XLSX file is indeed linked to the 3.2MB file of the Additional file 2 with the Figures S1 to S5. Therefore to access to the Additional file 1 download the XLXS file linked to the Additional file 2, and vice versa. Muriel GUGGER read full comment

Comment on: Calteau et al. BMC Genomics, 15:977

Comment from the authors: Incorrect ID number (Rayko Becher, 03 March 2015)

Sorry, for this delayed information! The AMADID number given in the original paper is incorrect. Due to submission problems, the Array design had to be re-uploaded resulting in a new ID number. The correct AMADID for the 8x15k Fusarium array used in this study is 038658. read full comment

Comment on: Becher et al. BMC Genomics, 12:52

Correction the City name (Jamal Sabir, 23 February 2015)

King Abdulaziz University is existing in the city of Jeddah not as appeared on the paper as Zeddah read full comment

Comment on: Tiwari et al. BMC Genomics, 15:273

Asking corrections (Tomohiro Yasuda, 17 February 2015)

I am the first author of this article. The published version of this article has problems, e.g., figures are shuffled and many of figures contain corrupted letters. I am asking corrections. Before the erratum of the article is available or corrections are incorporated,  a corrected PDF is available upon request to me. read full comment

Comment on: Yasuda et al. BMC Genomics, 16:S13

Link to Additional file 1 may be mislinked (Carrie Ganote, 12 February 2015)

This link:
Additional file 1. Summaries of SSR Table S1, SNP Table S2, and important genes Table S3 in the transcriptome of S. paramamosain.
It seems to contain 2 files, none of which are tables. Instead I see:
Fig. S1 The electrophoretic result of semi-quantitative PCR of Sp-VgR and Sp-18S rRNA from the green mud crab tissues.
Fig. S2 Expression pattern of Sp-gpr89 in different stages of developing ovaries by qRT-PCR
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Comment on: Gao et al. BMC Genomics, 15:585