FAQ

Database Contents
Org	Loci	Variations
Hs	23638	1307840
Mm	33230	120835
Rn	5943	13844
Dm	26367	42120
Ce	15741	1466

Frequently asked questions:

What is mutationdiscovery.com?
Who maintains this site?
Is there any charge for using this site?
Do I have to register?
Can other users see data that I've entered?

Why don't I see data that I've entered into mutationdiscovery.com?

What features are available with premium status?
Where does the information on this site come from?
How were the genes on this site selected?
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?
What are "Derived" features?
What does it mean when a source record is marked as "Status = Failed?"
Does this site include alternatively spliced transcripts for genes?
Will you be adding data from other organisms?
How can I obtain the mutationdiscovery genomic sequence for a locus?
What is DHPLC? And what is an amplicon?
Can I move amplicons I have designed on mutation discovery to my WAVE system?
What is SVG?
Is the Adobe SVG Plugin compatible with my computer?
Are there any known installation issues?
Known problems

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 Transgenomic, Inc. Many of Transgenomic'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 Transgenomic customers, so it is made available to scientific community as a whole.

For more information on Transgenomic, Inc., please visit www.transgenomic.com.

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 freely available.

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 mutationdiscovery@transgenomic.com.

7. What features are available with premium status?

Transgenomic 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 Transgenomic, Inc. and its customers.

Currently, data are gathered from:

Genome Annotation Project (NCBI)
Reference Sequence Project (NCBI)
dbSNP (NCBI)
GenBank / EMBL
LocusLink
OMIM

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 "mutationdiscovery.com Derived".

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 may be 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 Transgenomic web site ( www.transgenomic.com).

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 Transgenomic 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 SVG plug-in.

19. Is the Adobe SVG Plugin compatible with my computer?

Adobe's official list of system requirements can be found at

http://www.adobe.com/svg/systemreqs.html,

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 mid-September, 2002.

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
Macintosh Browsers:	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
Windows Browsers:	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?

Javascript
If you have disabled Javascript, you will need to enable it to complete the automated installation process. (You'll need Javascript anyway when you begin using the locus sequence display.)
Plugin
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.
Printing Problems
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.