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Title
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Finding Alu in primate genomes with AF-1
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Authors
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Ravi Shankar1*, Bhavesh Kataria1, Mitali Mukerji2
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Affiliation
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1Department of Bioinformatics & Structural Biology, School of Life Sciences & Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat (India) 382007; 2Functional Genomics Unit, 604-A, IGIB, CSIR, Mall Road, Delhi (India) 110007.
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Article Type
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Software
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Date
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received December 26, 2008; accepted January 27, 2009; published February 26, 2009
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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.
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Keywords |
Alu; algorithm; non-coding; primate; repetitive element
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| Availability |
AF1 is freely available at: http://software.iiar.res.in/af1/. The standalone is also available for download.
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Citation |
Shankar et al., Bioinformation 3(7): 287-288 (2009)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
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License
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This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
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