engleski

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

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 ten chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

ColorHOR ; alpha satellite ; higher order repeat ; HOR ; human genome ; DNA ; GenBank sequence ; computational genomics ; graphical user interface ; chromosome 1 ; 11mer ; key-string algorithm ; centromere

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