SCRMshaw: Supervised CRM Discovery
- SCRMshaw source code (Halfon lab GitHub repository)
- Utility program: "Get top hits"
- Utility program: "Cleanup /fasta directory"
- Utility program (for use in constructing new training sets): "SelectSmallestFeature.py"
- References:
- Kantorovitz, M.R., Kazemian, M., Kinston, S., Miranda-Saavedra, D., Zhu, Q., Robinson, G.E., Göttgens, B., Halfon, M.S.* and Sinha, S.* (2009). Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell, 17:568-579. PMID: 19853570. PMCID: PMC2768654. *co-corresponding authors
- Kazemian, M., Zhu, Q. , Halfon, M.S.*, Sinha, S*. (2011). Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucl. Acids Res., 39:9463-9472. doi: 10.1093/nar/gkr621. PMID: 21821659 PMCID: PMC3239187 *co-corresponding authors
- Kazemian, M.*, Suryamohan, K.*, Chen, J. *, Zhang, Y., Samee, M.A.H., Halfon, M.S.† and Sinha, S.† (2014). Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects. Genome Biology and Evolution, 6(9):2301-2320. doi: 10.1093/gbe/evu184. PMID: 25173756 PMCID: PMC4217690 *equal contribution, †co-corresponding authors
- Kazemian, M. and Halfon, M.S. (2019). CRM Discovery beyond model insects. Methods Mol. Biol., 1858:117-139. doi: 10.1007/978-1-4939-8775-7_10. PMID: 30414115
- Asma, Hasiba, and Halfon, M.S. (2019). Computational Enhancer Prediction: Evaluation and Improvements. BMC Bioinformatics 20:174. doi:10.1186/s12859-019-2781-x. PMID: 30953451
