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PROTEINS: Structure, Function, and Genetics 51:8595 (2003) BATMAS30: Amino Acid Substitution Matrix for Alignment of Bacterial Transporters Roman A. Sutormin,1* Aleksandra B. Rakhmaninova,2 and Mikhail S. Gelfand1,2 1 State Scientific Center GosNIIGenetica, Moscow, Russia 2 Integrated Genomics, Moscow, Russia ABSTRACT Aligned amino acid sequences of three functionally independent samples of transmembrane (TM) transport proteins have been analyzed. ... Most TM-kernels are central parts of TM-segments. ...
... According to the characteristic design of 2D walks we identify telomere sites, palindromes of various sizes and complexity, areas of ribosomal RNA, transposons, as well as diverse satellite sequences. ... Analysis of a large number of the different genomes shows that some chromosomes or their fragments of various species appear as imperfect gigantic palindromes, which are disintegrated by many inversions and the mutation drift on different scales. ... GENOME AS A 2D DNA WALK FIG. ... In Fig. ...