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Omplexity in terms of input sequence length, the time complexity of computing the combined profile kernels is also linear in sequence length.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptIn our experiments, kmin = 4 and kmax = 6 are chosen as the range of the k-mers by a crossvalidation on the SCOP bench mark dataset for remote homology detection (Kuang et al. 2005). Th
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E and protease family were predicted in accordance with the MEROPS classification system, and the enzyme was named in accordance with the SWISSPROT peptidase nomenclature (http://www.expasy.ch/cgi-bin/lists?peptidas.txt) and the literature. A Gene Ontology (GO) analysis was performed to predict the biological function, cellular process, and cellular location of the putative proteases (Ashburner et
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T.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) (Notredame, Higgins, and Heringa 2000), followed by manual inspection and editing. Graphic representations of the alignment and consensus sequences were deduced by the program BOXSHADE (http://www.ch.embnet.org/software/BOX_form.html). Phylogenetic trees were inferred by the neighbor-joining method using MEGA (http://www.megasoftware.net/) (Tamura et al.
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T.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) (Notredame, Higgins, and Heringa 2000), followed by manual inspection and editing. Graphic representations of the alignment and consensus sequences were deduced by the program BOXSHADE (http://www.ch.embnet.org/software/BOX_form.html). Phylogenetic trees were inferred by the neighbor-joining method using MEGA (http://www.megasoftware.net/) (Tamura et al.
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T.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) (Notredame, Higgins, and Heringa 2000), followed by manual inspection and editing. Graphic representations of the alignment and consensus sequences were deduced by the program BOXSHADE (http://www.ch.embnet.org/software/BOX_form.html). Phylogenetic trees were inferred by the neighbor-joining method using MEGA (http://www.megasoftware.net/) (Tamura et al.
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T.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi) (Notredame, Higgins, and Heringa 2000), followed by manual inspection and editing. Graphic representations of the alignment and consensus sequences were deduced by the program BOXSHADE (http://www.ch.embnet.org/software/BOX_form.html). Phylogenetic trees were inferred by the neighbor-joining method using MEGA (http://www.megasoftware.net/) (Tamura et al.
1
E and protease family were predicted in accordance with the MEROPS classification system, and the enzyme was named in accordance with the SWISSPROT peptidase nomenclature (http://www.expasy.ch/cgi-bin/lists?peptidas.txt) and the literature. A Gene Ontology (GO) analysis was performed to predict the biological function, cellular process, and cellular location of the putative proteases (Ashburner et
1
E and protease family were predicted in accordance with the MEROPS classification system, and the enzyme was named in accordance with the SWISSPROT peptidase nomenclature (http://www.expasy.ch/cgi-bin/lists?peptidas.txt) and the literature. A Gene Ontology (GO) analysis was performed to predict the biological function, cellular process, and cellular location of the putative proteases (Ashburner et