Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. It allows to exhaustively identify all the perfect and 1-error (where an error is defined to be a mismatch, insertion or deletion) matches of large sets of small RNAs to target sequences. Optimal performance is achieved at about 500000 query sequences
:: MORE INFORMATION
Berninger P, Gaidatzis D, van Nimwegen E, Zavolan M.
“Computational analysis of small RNA cloning data“,
Methods, 44(13-21), 2008