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https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#pairwise-alignment-algorithms
https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#combinatorial-extension-ce
Shindyalov and Bourne in 1998http://peds.oxfordjournals.org/content/11/9/739.short
http://www.ncbi.nlm.nih.gov/pubmed/9796821
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Wikipediahttp://en.wikipedia.org/wiki/Circular_permutation_in_proteins
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http://www.ncbi.nlm.nih.gov/pubmed/22496628
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org.biojava.nbio.structure.align.ce.CeCPMainhttp://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeCPMain.html
https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#fatcat---rigid
Yuzhen Ye & Adam Godzik in 2003http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii246.abstract
http://www.ncbi.nlm.nih.gov/pubmed/14534198
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http://www.ncbi.nlm.nih.gov/pubmed/7265238
org.biojava.nbio.structure.align.ce.CeCPMainhttp://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeCPMain.html
https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#other-methods
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https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#multiple-structure-alignment
Guda C, Scheeff ED, Bourne PE & Shindyalov IN in 2001http://psb.stanford.edu/psb-online/proceedings/psb01/abstracts/p275.html
http://www.ncbi.nlm.nih.gov/pubmed/11262947
org.biojava.nbio.structure.align.multiple.mc.MultipleMcMainhttps://www.biojava.org/docs/api/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.html
https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#creating-alignments-programmatically
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Structure Alignment Data Modelhttps://github.com/biojava/biojava-tutorial/blob/master/structure/alignment-data-model.md
https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md#acknowledgements
Homehttps://github.com/biojava/biojava-tutorial/blob/master/README.md
Book 3: The Structure Moduleshttps://github.com/biojava/biojava-tutorial/blob/master/structure/README.md
Chapter 7 : SEQRES and ATOM Recordshttps://github.com/biojava/biojava-tutorial/blob/master/structure/seqres.md
Chapter 9 : Biological Assemblieshttps://github.com/biojava/biojava-tutorial/blob/master/structure/bioassembly.md
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