Adz is a tool for identifying a sequence, like an adapter sequence for miRNA experiments, in another sequence, like reads from a miRNA experiment. Its efficiency is O(M * N) where M is the length of the longer sequence and N is the length of the shorter sequence.
Currently, it does not support insertions and deletions and only supports the FASTA with quality format from Illumina.
This code is experimental. Send questions, comments and bugs to brainarray at umich dot edu.
Download adzadapter 0.01 for Linux x86-64 here.
Use adz --help and adz --usage.