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1.
Figure 1.

Figure 1. From: Scoring profile-to-profile sequence alignments.

Scheme for profile–profile alignments.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.
2.
Figure 2.

Figure 2. From: Scoring profile-to-profile sequence alignments.

Comparison of seven scoring functions for profile–profile alignment. Choices at specific stages of the alignment process are listed at the top of the figure and described in Materials and Methods. (Upper left) QModeler scores; (upper right) QDeveloper scores; (lower left) QCombined scores; (lower right) search capability as measured by the number of true positives vs. false positives. The legend given in the lower left figure applies to all four plots.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.
3.
Figure 3.

Figure 3. From: Scoring profile-to-profile sequence alignments.

Comparison of Full Opt Gap Param vs. Fitted Gap Param for three scoring functions. Choices at specific stages of the alignment process are listed at the top of the figure and described in Materials and Methods. (Upper left) QModeler scores; (upper right) QDeveloper scores; (lower left) QCombined scores; (lower right) search capability as measured by the number of true positives vs. false positives. The legend given in the lower left figure applies to all four plots.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.
4.
Figure 5.

Figure 5. From: Scoring profile-to-profile sequence alignments.

Effect of adding secondary structure substitution matrix to three scoring schemes. Choices at specific stages of the alignment process are listed at the top of the figure and described in Materials and Methods. (Upper left) QModeler scores; (upper right) QDeveloper scores; (lower left) QCombined scores; (lower right) search capability as measured by the number of true positives vs. false positives. The legend given in the lower left figure applies to all four plots.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.
5.
Figure 4.

Figure 4. From: Scoring profile-to-profile sequence alignments.

Comparison of three weighting schemes and two sequence-choice schemes for the Log Odds Multin scoring function. Choices at specific stages of the alignment process are listed at the top of the figure and described in Materials and Methods. (Upper left) QModeler scores; (upper right) QDeveloper scores; (lower left) QCombined scores; (lower right) search capability as measured by the number of true positives vs. false positives. The legend given in the lower left figure applies to all four plots.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.
6.
Figure 6.

Figure 6. From: Scoring profile-to-profile sequence alignments.

Effect of combining protocol choices for all seven scoring functions. For the first three panels, “Combined” means taking the best scoring result of the seven scoring functions for each alignment pair. For the last panel, the scores of the seven functions were summed and used to sort the hits to form the true/false positive curve. Choices at specific stages of the alignment process are listed at the top of the figure and described in Materials and Methods. (Upper left) QModeler scores; (upper right) QDeveloper scores; (lower left) QCombined scores; (lower right) search capability as measured by the number of true positives vs. false positives. The legend given in the lower left figure applies to all four plots.

Guoli Wang, et al. Protein Sci. 2004 June;13(6):1612-1626.

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