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Bioinformatics Advance Access originally published online on October 27, 2004
Bioinformatics 2005 21(7):846-852; doi:10.1093/bioinformatics/bti072
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

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

*To whom correspondence should be addressed.

Motivation: GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been 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 the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a 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 detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the 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 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

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

Contact: paar{at}hazu.hr

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


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