T-RFPred

If you're looking for a tool to help you identify TRFLP fingerprint peaks using clone libraries of partially sequenced 16S rRNA genes, T-RFPred may be just what you need. This group of Perl scripts is designed to estimate the expected size of clone sequences based on a given restriction enzyme. In silico methods similar to this are essential to identify restriction fragment peaks.

T-RFPred operates by using the aligned Genbank version of the Ribosomal DataBase Project (RDP) which is reformatted to speed up the process. The method is based on the fact that often, only partial sequences are available in a clone library rather than the entire 16S rRNA gene. Additionally, the primer used for T-RFLP is usually the same as the one used for sequencing.

To estimate the length of the fragment, T-RFPred includes the length of the oligonucleotide, the estimated length of the "gap", and the length of the sample sequence from the beginning up to the first target size of the restriction enzyme. The length of the "gap" is estimated using a subset of the Ribosomal Database Project sequences that are long enough to span the oligonucleotide. A local BLASTN is then used to find the best hits, and Smith-Waterman alignments of the sample sequence and the best hits are used to give accurate percent similarities.

Lastly, T-RFPred provides the taxonomy of the closest relative. Overall, if you're a researcher looking for a tool to estimate the expected size of clone sequences and identify restriction fragment peaks in your TRFLP fingerprint analysis, T-RFPred may be a useful tool to consider.