Alan Moses' Computational Biology Lab
DNA and protein motif analysis tools


PhyloHMM website with data, software and supporting materials for conserved sequences in disordered regions (Nguyen Ba et al. 2012) Link to site.

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

NLStradamus is an HMM-based prediction method for the prediction of nuclear localization signals in proteins. Link to software.

Scripts to compute the statistical tests described in Moses BMC Evol. Biol. 2009 Link to software.

Find clusters of protein motifs as described in Moses et al. Genome Biol. 2007. Link to software.

EMnEM An EM algorithm for de novo DNA motif-finding in multiple alignments. Link to software.

MONKEY Programs to identify matches to DNA motifs in multiple alignments. Link to software.


Genomics and proteomics webservices and databases


Genome data for Ophiostoma Ulmi can be found here. Link to site.

SARB has genomic tools and resources for Saccharomyces arboricolus Link to site.

YeastKID A database of literature curated kinase-substrate interactions Link to database.

Use the SGRP website to search, extract and download data generated by SGRP. Link to site.


Other computational biology software

k-NN change detection for high-throughput, automated analysis of microscopy imagery.

Unsupervised clustering website with clustering results, data and image analysis software (Handfield et al.) Link to site.

Indelz A bioinformatics method to predict the effects of indels and non-sense mutations Link to software.

Data eater estimates sizes of yeast colonies in scanned images Link to software.






Alan Moses' Lab, Copyright 2009-2013.