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


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 -


Yeast Segmentation Web Tool

Got microscopy images of yeast cells that you need to segment? Upload your image(s) and get downloadable segmentation results within minutes.



IDR bioinformatics resources

Bioinformatics for IDRs is hard, especially compared to folded protein domains. Here are links to a number of useful online bioinformatics tools for IDRs that we (and our colleagues) have developed over the years.

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.