Transposable element identification tool
Python script to use blast to compare a directory of fasta sequence files to the transposable element database Repbase. Useful for quick identification of potential TEs in sequence sets that can be problematic for comparative analyses.
* [Python 2.7](http://www.python.org) * [Biopython](http://www.biopython.org) * [NCBI Blast+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) * [Repbase](http://www.girinst.org/repbase/) 1. Download [Repbase](http://www.girinst.org/repbase/) 2. Choose which files you want to include (ie: all of them, eukarotyoes only, only mice, etc.) 3. Place those files in a directory 4. Run `python convert-repbase.py` specifying the directory where you decompressed Repbase. 5. Build a blast DB with this fasta file: `makeblastdb -in REPBASE.FASTA -out XXXX -dbtype 'nucl'` 6. Run `python transeeker.py` specifying your new blastdb and a directory of sequence files in fasta format to check. 7. The results are in the form of a CSV file that can easily be parsed with code or opened in Excel, LibreOffice etc. 8. **Optional:** Run `python purge-hits.py` to remove all the hits from the original fasta files.