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Nucleic Acids Research 2005 33(Database Issue):D498-D500; doi:10.1093/nar/gki044
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Nucleic Acids Research, 2005, Vol. 33, Database issue D498-D500
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

L1Base: from functional annotation to prediction of active LINE-1 elements

Tobias Penzkofer2, Thomas Dandekar2 and Tomasz Zemojtel1,2,*

1 Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany and 2 Department of Bioinformatics, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany

* To whom correspondence should be addressed. Tel: +49 30 8413 1147; Fax: +49 30 8413 1152; Email: zemojtel{at}molgen.mpg.de

Received August 13, 2004; Revised and Accepted September 28, 2004

L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes that are as follows: (i) intact in the two open reading frames (ORFs), full-length L1s (FLI-L1s) and (ii) intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full-length (>6000 bp) non-intact L1s (FLnI-L1s) were also included in the database. Application of a novel annotation methodology, L1Xplorer, allowed in-depth annotation of functional sequence features important for L1 activity, such as transcription factor binding sites and amino acid residues. The L1Base is available online at http://l1base.molgen.mpg.de. In addition, the data stored in the database can be accessed from the Ensembl web browser via a DAS service (http://l1das.molgen.mpg.de:8080/das).

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