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. 2004 Sep 16;21(4):483–491. doi: 10.1093/bioinformatics/bti028

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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.

This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.

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Fig. 3 — SPAAN is a non-homology-based software program. A total of 130 adhesins and 130 non-adhesins were analyzed to assess whether the predictive power of SPAAN could be influenced by sequence relationships. (a) Histogram plots of the number of proteins in the various P_ad value ranges are shown. Shaded bars represent adhesins and open bars represent non-adhesins. Note the ability of SPAAN to segregate adhesins and non-adhesins into two distinct cohesive groups. (b) Pairwise sequence relationships among the adhesins were determined using CLUSTALW and plotted on x-axis. Higher CLUSTALW scores indicate similar pairs. The corresponding differences in P_ad values in the same protein pair was plotted on the y-axis. Each point in the diagram represents a pair. Arrow points to protein pairs of the FimH family with high ΔP_ad values in spite of high similarity. Since one of the FimH proteins (gi: 5524636) had very low P_ad value, all pairs with this false negative protein show high ΔP_ad values. The protein (gi: 5524636) is of much shorter length compared with other members of the same family. (c) Plot for non-adhesins. Data were plotted in the four-quadrant format to enhance clarity.