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Visualization of sequence and structural features of genomes and chromosome fragments. Application to CpG islands, Alu sequences and whole genomes
Subirana Torrent, Juan A.; Anokian, Ezequiel
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química
A very simple new program is presented (G-SQUARES). It is useful in order to visualize the composition and basic structural features of whole genomes and selected chromosome regions. The frequency of all dimer and tetramer sequences is reported. Overall structural features are calculated, such as the tendency for alternation. A direct visual comparison among different sequences is easily available. Furthermore, the features which are visualized indicate further studies which should be carried out. Examples are presented on Alu sequences, CpG islands, whole eukaryotic and bacterial genomes.
Àrees temàtiques de la UPC::Enginyeria química::Biotecnologia
DNA -- Structure -- Computer simulation
Genòmica -- Processament de dades
ADN -- Estructura -- Mètodes de simulació
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