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BMC Bioinformatics

, 6:158

First Online: 23 June 2005Received: 13 December 2004Accepted: 23 June 2005


BackgroundAll eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and the recently discovered autosome-specific Painting of Fourth POF protein in Drosophila. However, no sequences have been found that are chromosome-specific and distributed over the entire length of the respective chromosome. Here, we present a new, unbiased, exhaustive computational method that was used to probe three Drosophila genomes for chromosome-specific sequences.

ResultsBy combining genome annotations and cytological data with multivariate statistics related to three Drosophila genomes we found sequence signatures that distinguish Muller-s F-elements chromosome 4 in D. melanogaster from all other chromosomes in Drosophila that are not attributable to differences in nucleotide composition, simple sequence repeats or repeated elements. Based on these signatures we identified complex motifs that are strongly overrepresented in the F-elements and found indications that the D. melanogaster motif may be involved in POF-binding to the F-element. In addition, the X-chromosomes of D. melanogaster and D. yakuba can be distinguished from the other chromosomes, albeit to a lesser extent. Surprisingly, the conservation of the F-element sequence signatures extends not only between species separated by approximately 55 Myr, but also linearly along the sequenced part of the F-elements.

ConclusionOur results suggest that chromosome-distinguishing features are not exclusive to the sex chromosomes, but are also present on at least one autosome the F-element in Drosophila.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-6-158 contains supplementary material, which is available to authorized users.

Per Stenberg, Fredrik Pettersson contributed equally to this work.

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Autor: Per Stenberg - Fredrik Pettersson - Anja O Saura - Anders Berglund - Jan Larsson


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