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LOVD v.2.0 - Leiden Open Variation Database
Online gene-centered collection and display of DNA variations
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For all details about LOVD, see our LOVD flyer! (last updated February 24th, 2010) |
| Problems with mapping of variants to the genome |
2010-08-12 |
Yesterday a problem was discovered with the position converter part of Mutalyzer 2.0, that LOVD uses to map variants to the genome. For about a week, false positions may have been sent back to LOVD which leads to problems with for instance the link to the genome browsers. If in the last week you have added new variants, imported variants from a text file or edited the reference sequence information, the variant positions of the genes in question may be affected. To remap the variants in this specific gene database, follow these instructions:
- Make sure you are logged in as curator or higher user level.
- If not opened already, click on the "Configuration" tab.
- Make sure the correct gene is shown on the top of the page. If not, click the green switch icon and switch to the correct gene database from the list.
- Click the "Edit gene db" icon in the icon bar just below the menu tabs.
- Change the value of the "Human Build to map to (UCSC/NCBI)" field to "---- / non-Human", scroll to the bottom of the page, type in your password to authorize the changes, and submit the form.
- Edit the gene settings again, and change the human build value back to what it was, e.g. "hg19 / GRCh37".
- LOVD will now remap all the variants in this gene database.
Our apologies for the inconvenience. |
| LOVD 2.0 build 28 released |
2010-08-02 |
Today, LOVD 2.0-28 has been released. New features implemented, amongst others: Added a link to the Ensembl genome browser, when editing variants or patients the log entries now indicate what has changed, improved import file handling, improved the search functionalities by allowing for "phrase searching". Bugs fixed, amongst others: Fixed problem with the Copy Column feature, fixed security issue with public downloads of the unique variant overview, fixed notices when importing files with less data columns than header columns.
See the changelog.
Download the new build.
LOVD modules included: Mutalyzer 0.7, reCAPTCHA 0.1, ShowMaxDBID 0.4
LOVD scripts included: ParseRefSeq 2.13, Reading Frame Checker 1.0, UploadGenBank 1.5
Manual version included: August 2nd, 2010. |
| LOVD 2.0 build 27 released |
2010-07-05 |
Today, LOVD 2.0-27 has been released. New features implemented, amongst others: Managers can now also select curators for a gene, in stead of selecting genes for a curator; the list of curators on the gene homepage is now sortable and curators can be hidden from this list; added a couple of custom columns. Bugs fixed, amongst others: Non-numeric chromosome locations like 2q33-qter or 19cen-q13.1 are now also accepted as valid input; fixed problems with the validation of long DBID values; fixed data import problem that some users reported; relaxed the gene symbol check a bit, since the correct C#orf# gene symbols were rejected.
See the changelog.
Download the new build.
LOVD modules included: Mutalyzer 0.7, reCAPTCHA 0.1, ShowMaxDBID 0.4
LOVD scripts included: ParseRefSeq 2.13, Reading Frame Checker 1.0, UploadGenBank 1.5
Manual version included: April 12th, 2010. |
| Website LOVD 3.0 opened |
2010-05-19 |
| The website of LOVD 3.0 has been opened, almost 4 years after we opened the website for LOVD 2.0. There is no download or screenshots available yet, but you can expect some screenshots in the future before release. We are working hard on the software, but a first release will take at least 6 more months, so please be patient! More information on what will change in LOVD 3.0 versus LOVD 2.0, please visit the Frequently Asked Questions (FAQ). |
| LOVD 2.0 build 26 released |
2010-05-03 |
Today, LOVD 2.0-26 has been released. New features implemented, amongst others: The Find & Replace feature now also allows for "Field contains anything" type of matching, added support for NR reference sequences and the hg18 / NCBI Build 36.1, clarified how to submit homozygous variants on the variant submission form. Bugs fixed, amongst others: Fixed incorrect mutation count calculation, fixed lack of data verification when importing custom column data, data from public fields of patients with only non-public variants could be viewed, downloading and re-importing data containing quotes malformed these.
Closes #46.
See the changelog.
Download the new build.
LOVD modules included: Mutalyzer 0.7, reCAPTCHA 0.1, ShowMaxDBID 0.4
LOVD scripts included: ParseRefSeq 2.12, Reading Frame Checker 1.0, UploadGenBank 1.5
Manual version included: April 12th, 2010. |
| LOVD 2.0 build 25 released |
2010-03-15 |
Today, LOVD 2.0-25 has been released. New features implemented, amongst others: LOVD can import data from the HGNC when creating a new gene database, the submission page is redesigned to help users find their way, the Entrez Gene ID will also be provided by the LOVD API. Bugs fixed, amongst others: Internet Explorer couldn't hide the info boxes explaining the data displays, fixed problem with the reloading of the Mutalyzer module, fixed incomplete display of the variant statistics page, downloading variant and patient data ignored the search terms in the submitter ID field, submitters could not always see all variant data of patients submitted by them, fixed problem with curator authorization; curators could find a way to see hidden data from patients of other gene databases and they could find a way to see non-public variants from other genes.
See the changelog.
Download the new build.
LOVD modules included: Mutalyzer 0.7, reCAPTCHA 0.1, ShowMaxDBID 0.4
LOVD scripts included: ParseRefSeq 2.12, Reading Frame Checker 1.0, UploadGenBank 1.5
Manual version included: December 11th, 2009. |
News older than 6 months can be found in the archive.
| Last modified 2010/08/12 11:41:09 CEST |
When using or discussing LOVD please refer to:
Fokkema IFAC, Den Dunnen JT and Taschner PEM (2005). LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-Box" approach.
Hum Mutat. 2005 Aug;26(2):63-8.
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