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LOVD Manual

LOVD scripts

The public is encouraged to extend LOVD with useful scripts. If you are a programmer and you have written a script that you think is of use to other LOVD users, please contact me at I.F.A.C.Fokkema@LUMC.nl. Maybe we can add it to the next LOVD releases.


LOVD Reference Sequence Parser

The Reference Sequence Parser introduction page.
The Reference Sequence Parser introduction page.
LOVD currently comes with one script that is very useful if you want to create coding DNA reference sequences for the genes in your database. For it to work, you will need to make the refseq directory writable.

Making the refseq directory writable
Your LOVD package comes with a directory called 'refseq'. As explained above, this directory needs to be made writable. Below we will explain how to do that on Unix/Linux systems. If your LOVD is installed on a different server (Windows, Macintosh), please contact the person responsible for that server in order to make the directory world writable.

Information For advanced users
It is more secure to do a 'chgrp' on the folder to the user running the webserver, but you will need to do a 'ps' to find out which user that is (i.e. 'www-data' or 'httpd'). After that, make sure the groupbit has been set to 7 (rwx). This way, the Reference Sequence Parser works without making the refseq directory world writable.

Using the commandline
  • Log in to the server using SSH, telnet or any non-graphical (S)FTP client.
  • Move into the directory LOVD is placed using the 'cd' command.
  • Type in 'chmod 777 refseq'.
  • Check if the Reference Sequence Parser is still generating an error. If not, you're done.

Using a graphical (S)FTP client
Of course, there are so many different FTP clients that I can't write a exact manual on how to change rights on a folder. This will describe a generally used method.
  • Log in to the server using your favorite (S)FTP client.
    (FTP is a protocol used to transfer files to or from the internet. If you have uploaded your LOVD files to a server, you can use the same program you used then.)
  • Move into the directory LOVD is placed (usually by double clicking on the folder names).
  • Right click on the folder 'refseq', this will bring up a menu.
  • Select 'chmod' if it is an option. Otherwise, click 'Properties' and look for the folder permissions/rights.
  • Fill in '777' as the new value.
  • Check if the Reference Sequence Parser is still generating an error. If not, you're done.

Input formats Reference Sequence Parser
The Reference Sequence Parser accepts a specific input formats for each step. Step 2 requires the genomic sequence formatted to provide the positions of the upstream sequence, exons, introns, downstream sequence and the start of the translation.
Step 3 requires the coding DNA sequence formatted to provide the positions of the exon borders and the start of the translation.
Both formats are case-insensitive. It does not matter whether you use capital or non-capital nucleotides.

Input format for step 2
UPSTREAM<EXON>INTRON<EXON>INTRON<EXON>INTRON (...etc...) <EXON>DOWNSTREAM
Make sure you include the starting point of the translation by putting a '|' in front of the 'a' of the 'atg' starting codon.

Example:
cccccccc<gggggg|at>tttttttt<gggggggg>aaaaaaaa
will parse:
- 'cccccccc' as the upstream sequence.
- 'ggggggat' as exon 1, with the translation starting at the 'a'.
- 'tttttttt' as intron 1.
- 'gggggggg' as exon 2.
- 'aaaaaaaa' as the downstream sequence.

Step 2 will create the upstream sequence, intronic sequences and the downstream sequence and save them in the refseq directory. It will also create the input for step 3 for you.

Input format for step 3
EXON;EXON;EXON; (...etc...) ;EXON
Make sure you include the starting point of the translation by putting a '|' in front of the 'a' of the 'atg' starting codon.

Example:
gggggg|at;gggggggg
will parse:
- 'ggggggat' as exon 1, with the translation starting at the 'a'.
- 'gggggggg' as exon 2.

Step 3 will create the coding DNA sequence including the translation and save it in the refseq directory.

For examples on how these reference sequences will look like, take a look at the reference sequences www.DMD.nl, such as the CAPN3 reference sequence.

Last modified 2014/08/25 14:48:45


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.

Leiden University Medical Center, Netherlands
Ing. Ivo F.A.C. Fokkema, Dr. Johan T. den Dunnen