EFI-EST and Cytoscape Tutorials


1.Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC (2009) PLoS One 4, e4345.

2. Pythoscape: a framework for generation of large protein similarity networks. Barber AE 2nd, Babbitt PC (2012) Bioinformatics 28, 2845-6.

3. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Genome Res 13, 2498-504.

4. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Weizhong L, Godzik A (2006) Bioinformatics 22, 1658-9. 

5. CD-HIT: accelerated for clustering the next generation sequencing data. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) Bioinformatics 28, 3150-2.

6. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. (2015) Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics doi:10.1016/j.bbapap.2015.04.015


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