RESUMEN
SUMMARY: We have developed STAN (suffix-tree analyser), a tool to search for nucleotidic and peptidic patterns within whole chromosomes. Pattern syntax uses a string variable grammar-like formalism which allows the description of complex patterns including ambiguities, insertions/deletions, gaps, repeats and palindromes. STAN is based on a reduction to multipart matching on a suffix-tree data structure and can handle large DNA sequences, whether assembled or not.
Asunto(s)
Cromosomas/genética , Genómica/estadística & datos numéricos , Reconocimiento de Normas Patrones Automatizadas , Secuencia de Aminoácidos , Arabidopsis/genética , Secuencia de Bases , Cromosomas de las Plantas/genética , Biología Computacional , Elementos Transponibles de ADN/genética , ADN de Plantas/genética , Bases de Datos de Ácidos Nucleicos , Programas InformáticosRESUMEN
In the light of the recently published structure of GlpF and AQP1, we have analysed the nature of the residues which could be involved in the formation of the selectivity filter of aquaporins, glycerol facilitators and aquaglyceroporins. We demonstrate that the functional specificity for major intrinsic protein (MIP) channels can be explained on one side by analysing the polar environment of the residues that form the selective filter. On the other side, we show that the channel selectivity could be associated with the oligomeric state of the membrane protein. We conclude that a non-polar environment in the vicinity of the top of helix 5 could allow aquaglyceroporins and GlpF to exist as monomers within the hydrophobic environment of the membrane.
