Software

DNA and Protein Motif Analysis Tools

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

PhyloHMM

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

- Nguyen Ba et al. 2012 -

ConDens

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

- Lai et al. 2012 -

NLStradamus

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 -

EMnEM

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

- Moses et al. 2004 -

MONKEY

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 -

Genomics and Proteomics Webservices and Databases

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

OURB

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

- Khoshraftar et al. 2013 -

SARB

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

- Liti et al. 2013 -

YeastKID

A database of literature-curated kinase-substrate interactions.

- Sharifpoor et al. 2011 -

SGRP

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 -

Indelz

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.