Blocks Database review:

J.G. Henikoff & S. Henikoff, "Blocks database and its applications"
Meth. Enzy. 266:88-105 (1996).



Postscript and <A HREF="http://www.adobe.com/prodindex/acrobat/readstep.html">PDF</A> files of the following papers are available in this directory:

BLOCKS
S. Henikoff & J.G. Henikoff, "Automated assembly of protein blocks
for database searching", Nucl. Acids Res. 19:6565-6572 (1991).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=92093619">MEDLINE</A>

BLOSUM
---   "Amino acid substitution matrices from protein blocks" Proc 
Natl. Acad. Sci. USA, 89:10915-10919 (1992).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=93066354">MEDLINE</A>

MATRIX_TEST
---   "Performance evaluation of amino acid substitution matrices" 
Proteins 17:49-61 (1993).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=94052086">MEDLINE</A>

BLOCKSEARCH
---   "Protein family classification based on searching a database
of blocks." Genomics 19:97-107 (1994). 
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=94245187">MEDLINE</A>

BLOCKSEARCH_DNA
---   "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).

SEQUENCE_WEIGHTS
---   "Position-based sequence weights" J. Mol. Biol. 243:574-578 (1994).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=95055701">MEDLINE</A>

BLOCKMAKER
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.
<A HREF="http://www.elsevier.nl/journals/genecombis/preview/articles/0378111995004866/">Gene-COMBIS Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=96066614">MEDLINE</A>

BLOCKS_DB
S. Pietrokovski, J.G. Henikoff & S. Henikoff, "The Blocks database -
a system for protein classification" NAR 24:197-200 (1996).
<A HREF="http://www.oup.co.uk/nar/Volume_24/Issue_01/5s1011_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=96174629">MEDLINE</A>

PSEUDO_COUNTS
Jorja G. Henikoff and Steven Henikoff, "Using substitution probabilities
to improve position-specific scoring matrices", CABIOS 12:135-143(1996).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=8744776">MEDLINE</A>

APPLICATIONS
Jorja G. Henikoff and Steven Henikoff, "Blocks database and its applications",
Meth. Enzymol. 266, 88-105 (1996).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=96338735">MEDLINE</A>

RECENT_BLOCKS
J.G. Henikoff, S. Pietrokovski & S. Henikoff, "Recent enhancements to the
blocks database servers", Nucl. Acids Res. 25:222-226 (1997). 
<A HREF="http://www.oup.co.uk/nar/Volume_25/Issue_01/gka021_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=9016540">MEDLINE</A>

COBBLER
S. Henikoff & J.G. Henikoff, "Embedding strategies for effective use of
information from multiple sequence alignments", Protein Science 6:698-705
 (1997).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=97223837">MEDLINE</A>

BLOCKS_PERF
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). 
<A HREF="http://www.oup.co.uk/nar/Volume_26/Issue_01/gkb045_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=98062454">MEDLINE</A>

CODEHOP
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).
<A HREF="http://www.oup.co.uk/nar/Volume_26/Issue_07/gkb321_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=9512532">MEDLINE</A>

NEW_FEATURES
J.G. Henikoff, S. Henikoff &  S. Pietrokovski, "New features
of the Blocks Database servers", Nucl. Acids Res. 27:226-228 (1999). 
<A HREF="http://www.oup.co.uk/nar/Volume_27/Issue_01/gkc004_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=b&uid=9847186">MEDLINE</A>


BLOCKSPLUS
S. Henikoff, J.G. Henikoff & S. Pietrokovski, "Blocks+: A non-redundant database of
protein alignment blocks derived from multiple compilations",
Bioinformatics (to appear 1999).

INCREASED
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). 
<A HREF="http://www.oup.co.uk/nar/Volume_28/Issue_01/gkd025_gml.abs.html">NAR Article</A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=b&uid=10592233">MEDLINE</A>


Additional references:

LAMA
S. Pietrokovski, "Searching Databases of Conserved Sequence Regions by
Aligning Protein Multiple-Alignments", NAR 24:3836-3845 (1996).
<A HREF="http://www.oup.co.uk/nar/Volume_24/Issue_19/6s0225_gml.abs.html">NAR Article </A>
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=97025376">MEDLINE</A>

INTEIN_MOTIFS
Shmuel Pietrokovski, "Conserved sequence features of inteins (protein
introns) and their use in identifying new inteins and related
proteins", Protein Science 3:2340-2350 (1994).
<A HREF="http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=m&form=6&Dopt=r&uid=95276640">MEDLINE</A>
<A HREF="http://blocks.fhcrc.org/~pietro/inteins">More about Inteins</A>



URL http://blocks.fhcrc.org/