DNA and Protein Motif Analysis Tools

Software tools and services for sequence motif analysis, including clustering, classification, and prediction.


A phylogenetic hidden Markov model that generates accurate, specific predictions of functional elements in disordered regions. 

– Nguyen Ba et al. 2012 –


A bioinformatics method to predict the kinase substrates based on evolutionary conservation of consensus sites.

– Lai et al. 2012 –


An HMM-based prediction method for the prediction of nuclear localization signals in proteins.

– Nguyen Ba et al. 2009 –

Statistical Tests for Natural Selection in Regulatory Regions

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.

– Moses et al. 2009 –

Clusters of Protein Motifs

Scripts to find clusters of protein motifs that can be used to predict targets of cyclin-dependent kinase.

– Moses et al. 2007 –


A DNA motif finder that takes multiple alignments and a phylogenetic tree and identifies conserved patterns.

– Moses et al. 2004 –


A set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors.

– Moses et al. 2004 –

No Logo

No Logo is a statistical model for nuclear export signals (NESs).

Liku et al. 2018


Genomics and Proteomics Webservices and Databases

Databases and webservices for data generated from our genomics and proteomics research.


A data browsing utility for genome/proteome sequence and annotation data for Ophiostoma ulmi. 

– Khoshraftar et al. 2013 –


A data browsing utility for genome/proteome sequence and annotation data for Saccharomyces arboricolus.

– Liti et al. 2013 –


A database of literature-curated kinase-substrate interactions.

– Sharifpoor et al. 2011 –


A webservice that allows users to search, extract, and download data generated by the Saccharomyces Genome Resequencing Project.

– Bergström et al. 2014 –

– Liti et al. 2009 –

Other Computational Biology Software

kNN Change Detection

An unsupervised kNN Method to systematically detect changes in protein localization in high-throughput microscopy images. 

– Lu et al. 2016 –

Clustering of Protein Expression Patterns in Microscopy Images

A repository of clustering results, data, and image analysis software.

– Handfield et al. 2013 –


A webservice that implements a bioinformatics method to predict the effects of indels and non-sense mutations on genetic information.

– Zia et al. 2011 –

Data Eater

A Java program that estimates the sizes of yeast colonies in scanned images.