- 1. What is mutationdiscovery.com?
mutationdiscovery.com is a resource for people studying
genetic variation. The site includes the genomic DNA sequences of over
10,000 well-understood genes and information on variations that have
been observed on these genes. Within this context, the site also includes
PCR and DHPLC protocols for amplicons that have been used to screen subjects
for any of these variations.
- 2. Who maintains this site?
mutationdiscovery.com is built and maintained by
ADS Biotec, Inc. Many of ADS Biotec's customers work in the area of
mutation detection and screening and this site has been designed to help
them in their work. As a general collection of genetic variation data,
however, it can be useful to people other than ADS Biotec customers,
so it is made available to scientific community as a whole.
For more information on ADS Biotec, Inc., please
- 3. Is there any charge for using this site?
No, there is no charge for using this site. There are
some special features with restricted access, but the
basic sequence, variation and amplicon data are and will continue to be made
- 4. Do I have to register?
No. As mentioned above, access to basic
sequence, public variation and amplicon data are freely available
to anyone browsing the site. However, you cannot enter
or store your own data into the site until you register with
mutationdiscovery.com. Once you are registered, you may enter variation
and amplicon data which can be kept private (i.e., accessible only by
you) or can be shared with whomever you choose to grant access.
- 5. Can other users see data that I've entered?
By default all variation and amplicon data which you enter into mutation
discovery is private. You may, optionally, grant read-only access to
another user, or create groups of users and grant access to the group
as a whole. Only the original owner may change or delete data.
- 6. Why don't I see data that I've entered into
mutationdiscovery.com on the locus sequence display?
In order to see non-public data (i.e.,
data entered by private individuals) to which you have access you must
be logged on to mutationdiscovery.com. If you are still unable to see
your data once you are logged on please contact us at
- 7. What features are available with premium status?
ADS Biotec premium-status customers are given access to
Primer3-based amplicon design software and proprietary DHPLC melt profile analyses
specifically targeted toward WAVE™ technology.
- 8. Where does the information on this site come from?
The sequence and variation data on this site
are loaded from publicly available data sources, such as the National
Center for Biotechnology Information (NCBI) at the National Institutes
of Health. In building mutationdiscovery.com, we merge data from
these sources into a single, integrated view. DHPLC amplicon data comes
from ADS Biotec, Inc. and its customers.
Currently, data are gathered from:
- Genome Annotation Project (NCBI)
- Reference Sequence Project (NCBI)
- dbSNP (NCBI)
- GenBank / EMBL
To see the source of any information on the site,
click on the object in the locus display to call up the object's detail
window - the source of the data is listed on that page.
- 9. How were the genes on this site selected?
Our goal is to have sequence and variation data on
all known genes on this site. At this time, we extract our genomic foundation
sequence for each gene from the NCBI Genome Annotation Project contig
sequences. We build entries in our system for each of the genes on these
NCBI contigs that has an official or preferred gene symbol.
Over time, as these contigs (and their annotation)
are improved, more and more genes will meet our selection criteria and
we will load them onto this site. At this time, mutationdiscovery.com
includes only nuclear, protein coding genes and pseudogenes. Over time we
will add mitochondrial and non-coding genes.
- 10. How can I tell what sequences were used to create
the locus sequence display and which public sequences have been integrated
into the locus sequence display as variations?
To see what public data was used to create the locus sequence display for
any gene, click on the locus name in the upper right corner of the locus
sequence display to open the Locus Detail window. Click on the 'Sources'
tab to see a full list of all public sequence records considered when
building the locus.
The sequence record marked 'Primary' for the locus represents the sequence
record from which the mutationdiscovery.com reference sequence was taken.
Currently, all sequences for nuclearly-encoded genes are taken from NCBI's
Genome Annotation Project.
- 11. What are "Derived" features?
In the process of integrating public sequence records
with the mutationdiscovery.com locus sequence, incoming public sequence records
are aligned with the primary sequence and any sequence differences
identified are represented as variations on the mutationdiscovery.com locus sequence.
On the summary page for these features, the status is marked as
- 12. What does it mean when a source record is marked as "Status = Failed?"
In cases where we encounter problems trying to align
sequences with the primary locus sequence taken from the NCBI Genome Annotation Project,
or where ambiguous interpretation of differences between the sequences
exists, no variations are created for the incoming public record and that source
record is marked as "Status = Failed."
- 13. Does this site include alternatively spliced transcripts for genes?
In the locus sequence display various
gene models for the locus are represented as separate lines above the sequence bar.
Initially the model with the most exons is selected as current. An alternative
selected simply by clicking on the appropriate line. Transcriptions
shown in the sequence detail correspond to the currently selected gene model.
- 14. Will you be adding data from additional organisms?
The site currently contains gene and variation data for humans
and mice. We will be adding data for other organisms in
the near future. We started with human genes and variations because a
large percentage of DHPLC users are working on human genes and diseases,
but we also have many customers interested in other organisms.
- 15. How can I obtain the mutationdiscovery genomic sequence for a locus?
To obtain the genomic sequence for any
mutationdiscovery locus, go to the Locus Sequence Display and
click on the Sequence link located on the upper right corner
of the window.
- 16. What is DHPLC? And what is an amplicon?
DHPLC stands for "denaturing high performance
liquid chromatography", a technique for analyzing DNA sequence fragments.
An amplicon is a region of DNA that is amplified with PCR and then analyzed
using DHPLC. For more information on DHPLC, see the ADS Biotec web site
- 17. Can I move amplicons I have designed on mutation discovery to my WAVE system?
Amplicon definitions that you have created or which have been provided
by the staff at ADS Biotec may be downloaded into an XML formatted file by going to the Locus Sequence Display and
clicking on the Amplicon link located on the upper right corner
of the window.
If you are using WAVE™ DHPLC technology with Navigator™ software (v1.5.1 or greater),
this file may be imported directly to define methods for operating the instrument.
- 18. What is SVG?
The main locus display page on this site (
click here for a sample)
is built using technology called Scalable Vector Graphics
(SVG), an XML-based W3C standard for representing vector graphics.
From the official W3C overview:
SVG is a language for describing two-dimensional
graphics in XML. SVG allows for three types of graphic objects: vector
graphic shapes (e.g., paths consisting of straight lines and curves),
images and text. Graphical objects can be grouped, styled, transformed
and composited into previously rendered objects. Text can be in any XML
namespace suitable to the application, which enhances searchability and
accessibility of the SVG graphics. The feature set includes nested transformations,
clipping paths, alpha masks, filter effects, template objects and extensibility.
SVG drawings can be dynamic and interactive. The Document Object Model
(DOM) for SVG, which includes the full XML DOM, allows for straightforward
and efficient vector graphics animation via scripting. A rich set of event
handlers such as onmouseover and onclick can be assigned to any SVG graphical
object. Because of its compatibility and leveraging of other Web standards,
features like scripting can be done on SVG elements and other XML elements
from different namespaces simultaneously within the same Web page.
In most browsers (including IE and Netscape) it is necessary to install
a 3rd-party plug-in to view SVG pages.
The pages on this site should work with any
current SVG plug-in, but we only routinely test the site with the Adobe
- 19. Is the Adobe SVG Plugin compatible with my computer?
Adobe's official list of system requirements can be found at
but here's a quick summary. Note that this information applies
to version 3.0 of the Adobe SVG Plugin, and is current as of
|Macintosh Operating Systems:
OS 8.6 through 9.2, or OS 10.1 or later
OS 10.0 through 10.0.4 is NOT SUPPORTED
Microsoft IE 5 or higher, or Netscape 4.0 through 4.75
Netscape 6 is NOT SUPPORTED
|Windows Operating Systems:
Windows 95 or later, including 98, 98SE, NT, 2000, and XP
Windows NT requires Service Pack 4 or later
Netscape 4.0 through 4.75, or Microsoft IE 4 or later
Netscape 6 is NOT SUPPORTED
We have had good luck with Mozilla 0.9.9, but a manual installation is required.
Version 3.0 of the Adobe SVG Plugin DOES NOT WORK with Mozilla 1.0 and later.
In our limited experimentation with the Opera browser, we have not been able to get the Adobe SVG Plugin working.
- 20. Are there any known installation issues?
to complete the automated installation process. (You'll need
Refer to the previous paragraph to see if the Adobe SVG plugin is compatible
with your browser. This plugin is required to view sequence information.
Once you have downloaded the Adobe SVG plugin, you may have to restart
your browser or your computer before it begins working.
- 21. Known Problems
Exon Numbering Discrepancies
mutationdiscovery.com relies solely on the Genome Annotation Project's
annotation of exon boundaries and subsequently derives exon "numbers"
by counting 5' -> 3'. This may cause the mutationdiscovery.com exon
numbering to be different from acknowledged and/or published exon
naming conventions for some loci.
Problems printing the locus sequence display may be encountered
depending on the type and version of your browser. Problems may
include the inability to print any sequence region other than the
initial sequence region loaded when locus is first displayed,
and/or shrinking of the display to a single narrow column.