X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

Guest Blog: Rich Roberts Urges Scientists to ‘Think Methylation’ in Microbial Sequencing

Wednesday, October 21, 2015

Richard-Roberts-croppedRichard Roberts, Nobel Laureate and Chief Scientific Officer of New England Biolabs, offers his thoughts on the utility of methylation data for understanding prokaryotes. In his words:

“Please run SMRT Analysis to detect methylation in your prokaryotic PacBio data.

Most bacteria and archaea encode DNA methylases, many of which are known components of restriction-modification systems. Usually, these are quite specific in terms of the sequences they recognize; the restriction component becomes a key defense mechanism preventing phages, plasmids, and other DNA elements from infecting the cell.

Until recently, it was quite difficult to determine the recognition sequences of these methylases. For most organisms, we had no idea whether the genes we could detect in the genome were active or not. Now, thanks to the properties of the DNA polymerase used during SMRT Sequencing, we can accurately locate the positions of m6A and m4C along the genome and sometimes can deduce the position of m5C. By analyzing the sequence context of these modified bases, we can deduce motifs that are the recognition sequences for the various methylases encoded in the genomes. Increasingly, we can then accurately match the genes with the motifs they produce to enable precise, experimentally-determined annotation for those genes.

Further progress in this area will depend on our ability to gather as much experimental data as we can; to improve the algorithms for calling the motifs accurately from the raw PacBio reads; and to improve our ability to match the DNA methylase genes in a genome with the PacBio motifs that are found experimentally. The public availability of motif data produced by running SMRT Analysis after each PacBio run can be enormously beneficial. Even better, if the raw sequence reads are also available, then this can help the development of better algorithms for data interpretation.

There is another terrific use of the methylation data for anyone interested in trying to transform these strains: While the presence of methylated motifs — and hence methylase genes — does not mean that an active restriction system is present, very often it does, offering some information about how one might protect DNA to be used for transformation before it is introduced into the cell.

I encourage everyone to think ‘methylation’ when using PacBio systems to sequence bacterial and archaeal genomes. The current results of such methylation analysis can be found in REBASE by clicking on the blue PacBio icon. This also has a link through which you can submit your methylation motifs to REBASE.”

Subscribe for blog updates:

Archives