SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins . The GDE alignment format is one of the standard alignment formats. Popular programs for sequence alignment, e.g. ClustalW, can save alignment in this format. ... Sequences are placed one after another, the name of each sequence is placed onto a separate line and begins with ‘%’. ... Thus the alignment looks like this: . ... back to input format rules . ...
In Silico Biology 3 (2003) 197204 IOS Press 197 The Channel in Transporters is Formed by Residues That Are Rare in Transmembrane Helices Olga V. Kalinina1,*, Vsevolod J. Makeev1, Roman A. Sutormin1, Mikhail S. Gelfand1,2 and Aleksandra B. Rakhmaninova2 1 2 State Scientific Many genes encoding known or putative transport proteins are found in bacterial genomes. ... It is based on the analysis of amino acids frequencies in bacterial secondary transporters. ... Proteins 51, 8595. ...
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