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- Emergence of Protein Fold Families through Rational Design (2006) (Online version)
Feng Ding and Nikolay V Dokholyan, University of North Carolina at Chapel Hill
Diverse proteins with similar structures are grouped into families of homologs and analogs, if their sequence similarity is higher or lower, respectively, than 20%–30%. It was suggested that protein homologs and analogs originate from a common ancestor and diverge in their distinct evolutionary time scales, emerging as a consequence of the physical properties of the protein sequence space. Although a number of studies have determined key signatures of protein family organization...
- CorGen—measuring and generating long-range correlations for DNA sequence analysis (2006) (Online version)
Philipp W. Messer and Peter F. Arndt
CorGen is a web server that measures long-range correlations in the base composition of DNA and generates random sequences with the same correlation parameters. Long-range correlations are characterized by a power-law decay of the auto correlation function of the GC-content. The widespread presence of such correlations in eukaryotic genomes calls for their incorporation into accurate null models of eukaryotic DNA in computational biology...
- Bioinformatics and Computational Biology with Biopython (2003) (PDF, 72KB, 2pgs)
de Hoon et al., University of Tokyo
In recent years, high-level scripting languages such as Python, Perl, and Ruby have gained widespread use in bioinformatics. Python [3] is particularly useful for bioinformatics as well as computational biology because of its numerical capabilities through the Numerical Python project [1], in addition to the features typically found in scripting languages...
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