What is JAguc?
JAguc is a software for identifying large samples of RNA data efficiently. You put in sequences and get counts by species. While identification itself is done by Mega BLAST, JAguc takes care that no more searches are done than absolutely necessary. It also provides several nice and handy graphs and charts that visualize the obtained results.
When should I use it?
Whenever you have large samples of RNA sequences from a certain environment, want to know what creatures these are from and want to have this done automated and quickly, you can and probably should give JAguc a try.
How does it work?
JAguc applies a clustering algorithm to the filtered input sample based on pairwise semi-global alignments. Only the longest sequence of every cluster is then sent to Mega BLAST. This concept saves a lot of time compared to the naive approach. Read more here.
Why should I use it?
JAguc is a complete and plattform independent solution for the whole identification process. We know of no other single piece of software that does that. Besides, it is fast. If your are already conviced, go and get it here.
Who did it?
Supervised by Prof. Nebel, a project group of five created JAguc in the summer of 2009: Michael Holzhauser, Lars Hüttenberger, Raphael Reitzig, Matthias Sperber and Sebastian Wild. The underlying tool chain has been invented in collaboration with the ecology group at University of Kaiserslautern headed by Prof. Stoeck.