SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks

Bioinformatics
Gaurav SachdevaSrinivasan Ramachandran

Abstract

The adhesion of microbial pathogens to host cells is mediated by adhesins. Experimental methods used for characterizing adhesins are time-consuming and demand large resources. The availability of specialized software can rapidly aid experimenters in simplifying this problem. We have employed 105 compositional properties and artificial neural networks to develop SPAAN, which predicts the probability of a protein being an adhesin (Pad). SPAAN had optimal sensitivity of 89% and specificity of 100% on a defined test set and could identify 97.4% of known adhesins at high Pad value from a wide range of bacteria. Furthermore, SPAAN facilitated improved annotation of several proteins as adhesins. Novel adhesins were identified in 17 pathogenic organisms causing diseases in humans and plants. In the severe acute respiratory syndrome (SARS) associated human corona virus, the spike glycoprotein and nsps (nsp2, nsp5, nsp6 and nsp7) were identified as having adhesin-like characteristics. These results offer new lead for rapid experimental testing. SPAAN is freely available through ftp://203.195.151.45 ramu@igib.res.in.

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Citations

Jul 10, 2012·Briefings in Bioinformatics·Tulika Prakash, Todd D Taylor
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Software Mentioned

BLASTP
- BLASTP
CLUSTALW
Conserved Domain Database search ( RPS
Hat
Red
Linux
BETAWRAP
SPAAN

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