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.
ConDens
A bioinformatics method to predict the kinase substrates based on evolutionary conservation of consensus sites.
NLStradamus
An HMM-based prediction method for the prediction of nuclear localization signals in proteins.
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.
Clusters of Protein Motifs
Scripts to find clusters of protein motifs that can be used to predict targets of cyclin-dependent kinase.
EMnEM
A DNA motif finder that takes multiple alignments and a phylogenetic tree and identifies conserved patterns.
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.
Webservices and Databases
Databases and webservices for data generated from our genomics and proteomics research.
SARB
A data browsing utility for genome/proteome sequence and annotation data for Saccharomyces arboricolus.
SGRP
A webservice that allows users to search, extract, and download data generated by the Saccharomyces Genome Resequencing Project.
YeastSpotter
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.
https://doi.org/10.1093/bioinformatics/btz402
Other Computational Biology Software
kNN Change Detection
An unsupervised kNN Method to systematically detect changes in protein localization in high-throughput microscopy images.
Clustering of Protein Expression Patterns in Microscopy Images
A repository of clustering results, data, and image analysis software.