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Update alignment.md
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structure/alignment.md

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@@ -129,7 +129,7 @@ BioJava class: [org.biojava.bio.structure.align.fatcat.FatCatFlexible](www.bioja
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### Smith-Waterman
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This aligns residues based on Smith and Waterman's 1981 algorithm for local
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*sequence* alignment. No structural information is included in the alignment, so
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*sequence* alignment [![pubmed](http://img.shields.io/badge/in-pubmed-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/7265238). No structural information is included in the alignment, so
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this only works for proteins with significant sequence similarity. It uses the
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Blosum65 scoring matrix.
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