1. How can I find all retrotransposon species that are significantly overrepresented
in the binding sites of a given transcription factor?
RTFAdb offers a simple yet functional user interface for the search operations. Just simply use an appropriate search module for your question and define your search parameters with pulldown menus. Then submit your query. Retrieving the results from RTFAdb may take a few seconds.
2. How can I manage my search results?
Your search results are provided in a searchable and sortable table. They are also downloadable as tab-delimited text file and portable network graphics formats.
3. Can I download the genomic intervals of retrotransposons that intersect with transcription factor binding sites?
Yes, you can download the genomic intervals in BED file format from the file annotation table in the results page.
4. Which genome assemblies and repeat element annotations did we use for the prediction of retrotransposon - transcription factor associations?
We utilized hg19 and mm10 genome assemblies for human and mouse, respectively, while developing RTFAdb database. We retreived all repeat element annotations from UCSC Genome Browser. Human annotation was downloaded from here and mouse repeat annotation derived from here.