Finding Alu in primate genomes with AF‐1

Repetitive sequences occupy more than 40% of the human genome which is much larger compared to the 2% occupied by the coding DNA. Amongst these Alu elements are the second largest class of repeats, occupying nearly 10% of the whole genome. Alus have been implicated in many genomic processes, sometimes giving rise to aberrations while many times playing as silent player in genomic and regulatory evolution. Here we present a web server, AF1, exclusively developed for finding Alu like elements. Besides alignment based methodology, this server utilizes probabilistic scanning to find more diverged elements and employs a more precise way of element classification based on unequal weighting of sequence through sequence encoding. AVAILABILITY: AF1 is freely available at http://software.iiar.res.in/af1/. The standalone is also available for download.