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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  http://nar.oxfordjournals.org/content/early/2015/01/10/nar.gku1397.full 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 http://osa-bioinform.uhmc.sunysb.edu/mlpa2/cgi-bin/mlpa.cgi   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: http://bioinfo-ccb.usm.my/cgi-bin/gb2/gbrowse/Rubber/ 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 http://dx.doi.org/10.1016/j.fgb.2008.04.005... 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
read full comment

Comment on: Gao et al. BMC Genomics, 15:585

How the PCR amplification performed? (Ren-Gang Zhang, 20 January 2015)

I am a reader. The first paragraph at Page 10 of 13 showed that the non-phosphorylated adapters were used. Thus, after ligation of digested DNA and adaptors, there should be two nicks on one DNA ligation product (Figure below). Between the steps of ligation and PCR amplification, there was no step to repair the nicks (see the 2b-RAD protocol of the paper). So comes the question, how the primers that annealed to the bottom adaptor extended (Figure below), as the PCR condition was: 98℃ for 30 s followed by 12 cycles of 98℃ for 30 s, 65℃ for 30 s, 72℃ for 30 s with a final Taq extension step at 72℃ for 5... read full comment

Comment on: Guo et al. BMC Genomics, 15:956

Update to Addtl. file 2 by the authors. (Lex Flagel, 03 December 2014)

When creating Addtl. file 2 we inadvertently omitted several unigene sequences.  The complete set of unigene sequences can be downloaded from the link below: http://goo.gl/TlZmgT note the fasta file is compressed with bzip2. read full comment

Comment on: Flagel et al. BMC Genomics, 15:195

Figures in "Evaluation of variant identification methods for whole genome sequencing data in dairy cattle" (Christine Baes, 27 November 2014)

The online html version of the online paper (http://www.biomedcentral.com/1471-2164/15/948) is wrong: the figures are incorrectly numbered, beginning with Figure 1, which is actually missing. This numbering problem runs through all Figures, and the figures 9 and 10 are the same. Please download the .pdf version of the paper for the correct figures. The editorial board has been contacted.   read full comment

Comment on: Baes et al. BMC Genomics, 15:948

Errata for SupFig6.docx and SupT2.xlsx. (Juha Immanen, 27 November 2014)

Some PpRRs have different name in main manuscript and in supplementary files. SupFig6.docx and SupT2.xlsx PpRR name should be changed like this: PpRR2 to PpRR8 PpRR3 to PpRR9 PpRR4 to PpRR11 PpRR5 to PpRR18 PpRR6 to PpRR12 PpRR7 to PpRR14 PpRR8 to PpRR16 PpRR9 to PpRR17 PpRR10 to PpRR21   read full comment

Comment on: Immanen et al. BMC Genomics, 14:885

NRRL 62431 misidentification (Toni Gabaldon, 27 November 2014)