# Blocks Manuscripts

S. Henikoff & J.G. Henikoff, "Automated assembly of protein blocks for database searching", Nucl. Acids Res. 19:6565-6572 (1991).
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S. Henikoff & J.G. Henikoff, "Amino acid substitution matrices from protein blocks" Proc Natl. Acad. Sci. USA, 89:10915-10919 (1992).
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S. Henikoff & J.G. Henikoff, "Performance evaluation of amino acid substitution matrices" Proteins 17:49-61 (1993).
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S. Henikoff & J.G. Henikoff, "Protein family classification based on searching a database of blocks." Genomics 19:97-107 (1994).
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S. Henikoff & J.G. Henikoff, "A Protein Family Classification Method for Analysis of Large DNA Sequences." Proceedings of the 27th Ann. Hawaii Intl. Conf. on System Sciences pp. 265-274 (1994).
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S. Henikoff & J.G. Henikoff, "Position-based sequence weights" J. Mol. Biol. 243:574-578 (1994).
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S. Henikoff, J.G. Henikoff, W.J. Alford & S. Pietrokovski, "Automated construction and graphical presentation of protein blocks from unaligned sequences". Gene-COMBIS, Gene 163 (1995) GC17-26.
PubMed Gene-COMBIS Article Postscript PDF

S. Pietrokovski, J.G. Henikoff & S. Henikoff, "The Blocks database - a system for protein classification" NAR 24:197-200 (1996).
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Jorja G. Henikoff and Steven Henikoff, "Using substitution probabilities to improve position-specific scoring matrices", CABIOS 12:135-143(1996).
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S. Pietrokovski, "Searching Databases of Conserved Sequence Regions by Aligning Protein Multiple-Alignments", NAR 24:3836-3845 (1996).
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Jorja G. Henikoff and Steven Henikoff, "Blocks database and its applications", Meth. Enzymol. 266, 88-105 (1996).
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J.G. Henikoff, S. Pietrokovski & S. Henikoff, "Recent enhancements to the blocks database servers", Nucl. Acids Res. 25:222-226 (1997).
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S. Henikoff & J.G. Henikoff, "Embedding strategies for effective use of information from multiple sequence alignments", Protein Science 6:698-705 (1997).
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S. Henikoff, S. Pietrokovski & J.G. Henikoff, "Superior performance in protein homology detection with the Blocks Database servers", Nucl. Acids Res. 26:309-312 (1998).
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T.M.Rose, E.R.Schultz, J.G.Henikoff, C.M.McCallum & S. Henikoff, "Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly-related sequences", Nucl. Acids Res. 26:1628-1635 (1998).
PubMed NAR Article Postscript PDF

J.G. Henikoff, S. Henikoff & S. Pietrokovski, "New features of the Blocks Database servers", Nucl. Acids Res. 27:226-228 (1999).
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S. Henikoff, J.G. Henikoff & S. Pietrokovski, "Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations", Bioinformatics 15:471-9 (1999).
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J.G. Henikoff, E.A. Greene, S. Pietrokovski & S.Henikoff, "Increased coverage of protein families with the blocks database servers", Nucl. Acids Res. 28:228-230 (2000).
PubMed NAR Article

S. Henikoff and J.G. Henikoff, "Amino acid substitution matrices", Adv. Protein Chem. 54:73-97 (2000).
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P.C. Ng, J.G. Henikoff & S. Henikoff, "PHAT: a transmembrane-specific substitution matrix" Bioinformatics 16:760-6 (2000).
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P.C. Ng & S. Henikoff "SIFT: Predicting amino acid changes that affect protein function", NAR, 31.13:3812-3814 (2003).
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T.M Rose, J.G. Henikoff & S. Henikoff "CODEHOP PCR Primer Design", NAR, 31.13:3763-3766 (2003).
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