CBU - Computational Biology Unit

Lipo can analyse polypeptide sequences encoded within the genome of Gram-negative bacteria and report the sequences with a possible lipo-box. The lipo-box is recognised on the basis of the critera given by Lipo.

Frode Berven (C) 2004

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Scoring system

We also developed a scoring system that reflects the similarity of the lipo-box of the predicted lipoprotein to the lipo-boxes of the 183 lipoproteins found in Swiss-Prot. The frequency of each amino acid in each position in the 183 known lipo-boxes was calculated. The score of the lipo-box of the predicted lipoprotein was calculated by summarising the frequency value of each amino acid in the lipo-box. The predicted lipoproteins were divided into three categories; high, medium, and low based on empirically found score thresholds.

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