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. 2012 Jan;40(Database issue):D252-60.
doi: 10.1093/nar/gkr1189. Epub 2011 Dec 6.

Minimotif Miner 3.0: Database Expansion and Significantly Improved Reduction of False-Positive Predictions From Consensus Sequences

Free PMC article

Minimotif Miner 3.0: Database Expansion and Significantly Improved Reduction of False-Positive Predictions From Consensus Sequences

Tian Mi et al. Nucleic Acids Res. .
Free PMC article


Minimotif Miner (MnM available at or is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease.


Figure 1.
Figure 1.
Revised minimotif model. The key elements of the minimotif syntax are colored blue. Orange boxes indicate attributes that are unique to specific minimotif triplets. Yellow ovals are for different attributes of minimotif triplet elements. All attributes except those in the purple boxes were previously described in our minimotif model and the purple boxes are new attributes to define motif modifications and activity modifications (12).
Figure 2.
Figure 2.
Screenshot of minimotif filter selection page. Screenshot of MnM 3 filter section for choosing approaches for filtering out false-positive minimotifs.
Figure 3.
Figure 3.
Results table in MnM 3 from analysis of HIV-1 Nef protein. Nef (NP_057857) was analyzed to produce the minimotif predictions shown. Column 1 shows the minimotif sequence, column 2 shows the function of the minimotif, column 3 shows the amino acid position(s) for the start residue in the minimotif, column 4 shows the combined filter score, and column 5 shows the number of occurrences of each motif in the entire HIV-1 proteome. Rows colored blue are for minimotifs that are experimentally validated, yellow are above a threshold for high accuracy prediction, and red are below this threshold or do not have data to calculate a combined filter score (null).

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