Abstract
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. AF1 is freely available at http://software.iiar.res.in/af1/. The standalone is also available for download.
Highlights
Alus are short interspersed nucleotide elements, which Restricted alignment based module (2) Probabilistic comprise about 10% of human genome (International modeler (3) Classifier
An intact Alu has two FASTA format either in paste sequence mode or load monomeric units linked through an A-rich region, with sequence file mode
The input query sequence is elements is estimated to be 282 base pairs excluding searched for exact match seed using library of overlapping variable length 3' poly-A tail. These repeats harbor words generated from an Alu prototype sequence unlike regulatory sites and contribute to the regulatory repertoire any other database search tools that instead break query of the genome [1, 2]
Summary
Background: Alus are short interspersed nucleotide elements, which Restricted alignment based module (2) Probabilistic comprise about 10% of human genome (International modeler (3) Classifier. The input query sequence is elements is estimated to be 282 base pairs excluding searched for exact match seed using library of overlapping variable length 3' poly-A tail. These repeats harbor words generated from an Alu prototype sequence unlike regulatory sites and contribute to the regulatory repertoire any other database search tools that instead break query of the genome [1, 2].
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