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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti072
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 12, 2004
Revised September 15, 2004
Accepted September 15, 2004

Article

ColorHOR - novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome

Vladimir Paar 1*, Nenad Pavin 1, Marija Rosandic 2, Matko Gluncic 1, Ivan Basar 1, Robert Pezer 1, and Sonja Durajlija Zinic 3

1 Faculty of Science, University of Zagreb, Bijenicka 32, 10000 Zagreb, Croatia
2 Department of Internal Medicine, University Hospital Rebro, Kispaticeva 12, Zagreb, Croatia
3 Ruder Boskovic Institute, Bijenicka 54, Zagreb, Croatia

* To whom correspondence should be addressed.
Vladimir Paar, E-mail: paar{at}hazu.hr


  Abstract

Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths were not reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences.

Results: We develop a graphical user interface method ColorHOR for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on composition of genomic sequence. ColorHOR is based on extension of the key-string algorithm (KSA) and provides a color representation of the order and orientation of HORs. For the key string we use a robust 6-bp string from consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more details, first we illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11, and 19. For the first time, we determine exact consensus lengths of HORs in ten chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into GenBank database.

Availability: The program with graphical user interface application for ColorHOR is freely available at www.hazu.hr/KSA/colorHOR.html. It can be run on any platform where wxPython is supported.

Supplementary information: www.hazu.hr/KSA/colorHOR.html.


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