Bibliographies |
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Databases & Logic
Programming Bibliography
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maintained by Michael Ley |
A Collection of Computer Science Bibliographies (Canadian Mirror) |
more than one million of CS BibTeX references |
Sequence Alignment, Analysis and Comparison: a bibliography |
1,760 entries by William H. E. Day |
MathSciNet |
AMS bibliography on-line |
Networked Computer Science Technical Reports Library |
(NCSTRL) |
Computer Science Research Paper Search Engine |
Yahoo-style search engine for CS papers |
ResearchIndex |
over 7 millions pages and 5 millions citations |
ACM Computing Research Repository |
(CoRR) |
IEEE bibliographies on-line |
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Benno's Computer Science Bio-Digest |
a regular survey of some CS journals for articles related to the field of Computational Biology |
A bibliography on stringology |
by T. Lecroq |
The Hypertext Bibliography Project |
by David M. Jones |
A bibliography on computational gene recognition |
by Wentian Li |
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Groups and link collections |
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Theoretical Computer Science On The Web |
maintained by Suresh Venkat |
Pattern Matching & Data Mining Research Group Homepage |
maintained by Mika Klemettinen and Jaak Vilo |
Human Genome Most Used Links |
hosted at LANL |
Complexity Related Links |
maintained by Bruce Edmonds |
ACM SIGACT |
Special Interest Group on Algorithms and Computation Theory |
Theoretical Computer Science Genealogy |
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TCS: virtual address book |
lists URLs of 1105 theoretical computer scientists around the world |
A compendium of NP optimization problems |
maintained by P. Crescenzi and V. Kann |
Knowledge Discovery Nuggets Directory:
Data Mining and Knowledge Discovery Information |
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The Bioinformatics Resources |
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The Rewriting Page |
maintained by Nachum Dershowitz and Laurent Vigneron |
Amos' WWW links page |
maintained by Amos Bairoch |
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Books |
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Pattern Matching Algoritms |
Alberto Apostolico, Zvi Galil, eds. |
Bioinformatics: The Machine Learning Approach | Pierre Baldi, Soren Brunak |
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins |
Andreas Baxevanis, B.F.Francis Ouellette (Eds.) |
Computational Molecular Biology: An Introduction |
Peter Clote, Rolf Backofen |
Algorithms on Strings |
Maxime Crochemore, Christophe Hancart, Thierry Lecroq |
Text Algorithms |
Maxime Crochemore, Wojciech Rytter |
Jewels of Stringology |
Maxime Crochemore, Wojciech Rytter |
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids |
Richard Durbin (Editor), S. Eddy, A. Krogh, G. Mitchison |
Information Retrieval Data Structures & Algorithms |
Bill Frakes, Ricardo Baeza-Yates (eds.) |
Developing Bioinformatics Computer Skills |
Cynthia Gibas, Per Jambeck |
Handbook of Algorithms and Data Structures |
Gaston H. Gonnet, Ricardo Baeza-Yates |
Combinatorics on Words |
M. Lothaire |
Algebraic Combinatorics on Words |
M. Lothaire |
Applied Combinatorics on Words |
M. Lothaire |
Algorithms on Strings, Trees and Sequences |
Dan Gusfield |
Rewriting Solving Proving |
Claude Kirchner, Helene Kirchner |
Bioinformatics: Sequence and Genome Analysis |
David Mount |
Introduction to Computational Molecular Biology |
João Meidanis & João Carlos Setubal |
Pattern Discovery in Bioinformatics: Theory & Algorithms |
Laxmi Parida |
Computational Molecular Biology: An Algorithmic Approach |
Pavel A. Pevzner |
Flexible Pattern Matching in Strings |
Gonzalo Navarro and Mathieu Raffinot |
Computational Methods in Molecular Biology |
Steven Salzberg, David Searls, Simon Kasif (eds.) |
String Searching
Algorithms |
Graham A. Stephen |
Pattern Discovery in Biomolecular Data |
Jason Wang, Bruce A. Shapiro, Dennis Shasha (eds.) |
Introduction To Computational Biology |
Michael Waterman |
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Journals |
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Theory Calendar - Journal Calls |
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ACM: Digital Library |
LOTS of papers on line |
ACM Transactions on Algorithms (TALG) |
papers on line |
IEEE OPeRA (Online Periodicals and Research Area) |
LOTS of papers on line |
IEEE conference proceedings on-line |
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Algorithmica |
papers on line |
BMC Bioinformatics |
papers on line |
Bioinformatics (formerly CABIOS) |
papers on line |
Chicago Journal of Theoretical Computer Science |
papers on line |
Combinatorics, Probability and Computing |
papers on line |
Complexity |
papers on line |
Data Mining and Knowledge Discovery |
abstracts on line |
Discrete Applied Mathematics |
abstracts on line |
Discrete Mathematics and Theoretical Computer Science |
papers on line |
Electronic Journal of Combinatorics |
papers on line |
European Journal of Combinatorics |
abstracts on line |
Genome Research |
papers on line |
Genome Biology |
papers on line |
Journal of ACM
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papers on line |
Journal of Algorithms
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papers on line |
Journal of Bioinformatics and Computational Biology |
papers on line |
Journal of Computational Biology |
recent papers online |
Journal of Complexity |
abstracts on line |
Journal of Molecular Biology |
papers on line |
Journal of Experimental Algorithmics |
papers on line |
Journal of Universal Computer Science
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papers on line |
Journal of Graph Algorithms and Applications
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papers on line |
IEEE Transactions on Information Theory |
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IEEE Transactions on Knowledge and Data Engineering |
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Information and Computation (or here) |
abstract on line |
Informatica |
abstract on line |
Information Processing Letters |
papers on line |
International Journal of Bioinformatics Research and Applications |
papers on line |
International Journal of Data Mining and Bioinformatics |
papers on line |
Lecture Notes in Computer Science |
papers on line |
Nucleic Acid Research |
papers on line |
Nordic Journal on Computing |
abstracts on line |
SIAM Journal on Computing |
papers on line |
SIGACT News Online |
papers on line |
Theoretical Computer Science |
papers on line |
IEEE/ACM Transactions on Computational Biology and Bioinformatics |
papers on line |
The Computer Journal |
papers on line |
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Proceedings |
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Bio-Informatics and Biomedical Engineering (BIBE) |
papers on line (2001) |
Bio-Informatics and Biomedical Engineering (BIBE) |
papers on line (2003) |
Bio-Informatics and Biomedical Engineering (BIBE) |
papers on line (2004) |
BIOKDD |
papers on line (2001) |
BIOKDD |
papers on line (2002) |
IEEE Computer Society Bioinformatics Conference (CSB) | papers on line (2003) |
IEEE Computer Society Bioinformatics Conference (CSB) |
papers on line (2002) |
Combinatorial Pattern Matching (CPM) |
papers on line (2007) |
Combinatorial Pattern Matching (CPM) |
papers on line (2005) |
Combinatorial Pattern Matching (CPM) |
papers on line (2004) |
Combinatorial Pattern Matching (CPM) |
papers on line (2003) |
Combinatorial Pattern Matching (CPM) |
papers on line (2002) |
Combinatorial Pattern Matching (CPM) |
papers on line (2001) |
Combinatorial Pattern Matching (CPM) |
papers on line (2000) |
Combinatorial Pattern Matching (CPM) |
papers on line (1999) |
Compression and Complexity of Sequences (SEQUENCES) |
papers on line (1997) |
Computational System Bioinformatics (CSB) |
papers on line (2003-) |
Data Compression Conference (DCC) |
papers on line (1991-) |
European Conference on Computational Biology (ECCB) |
papers on line (2002) |
European Conference on Computational Biology (ECCB) |
papers on line (2003) |
European Conference on Computational Biology (ECCB) |
papers on line (2004) |
Foundations of Computer Science (FOCS) |
papers on line (1996-) |
Genome Informatics
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papers on line (1996-) |
Intelligent Systems for Molecular Biology (ISMB) |
papers on line (2004) |
Intelligent Systems for Molecular Biology (ISMB) |
papers on line (2003) |
Intelligent Systems for Molecular Biology (ISMB) |
papers on line (2002) |
Intelligent Systems for Molecular Biology (ISMB) |
papers on line (2001) |
Intelligent systems for Molecular Biology (ISMB) |
papers on line (2000) |
Pacific Symposium on Biocomputing (PSB) |
papers on line (1996-) |
Principles of Programming Languages (POPL) |
papers on line (1987-) |
Research in Computational Molecular Biology (RECOMB) |
papers on line (1997-2004) |
Research in Computational Molecular Biology (RECOMB) |
papers on line (2008) |
Research in Computational Molecular Biology (RECOMB) |
papers on line (2005) |
Research in Computational Molecular Biology (RECOMB) |
papers on line (2006) |
String Processing and Information Retrieval Symposium (SPIRE) |
papers on line (1998) |
String Processing and Information Retrieval Symposium (SPIRE) |
papers on line (1999) |
String Processing and Information Retrieval Symposium (SPIRE) |
papers on line (2000) |
String Processing and Information Retrieval Symposium (SPIRE) |
papers on line (2001) |
String Processing and Information Retrieval Symposium (SPIRE) |
papers on line (2004) |
Symposium on Discrete Algorithms (SODA) |
papers on line (1997-) |
Symposium on Theory of Computing (STOC) |
papers on line (1985-) |
Algorithms in Bioinformatics: 5th International Workshop (WABI) |
papers on line (2005) |
Algorithms in Bioinformatics: 4th International Workshop (WABI) |
papers on line (2004) |
Algorithms in Bioinformatics: 3rd International Workshop (WABI) |
papers on line (2003) |
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Software |
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Exact string matching algorithms in Java |
by Christian Charras - Thierry Lecroq |
Information Retrieval Projects |
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PERL |
the "information extraction" language |
The LEDA Library |
Library of Efficient Datatypes and Algorithms |
The Stony Brook Algorithm Repository |
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GLIMPSE and AGREP |
A tool to search entire file systems |
HARVEST |
Information Discovery and Access System |
AGREP for DOS, OS/2 and Windows 95/NT |
(not yet GLIMPSE) |
GAIS |
A General-Purposed Information Discovery System |
Handbook of Algorithms and Data Structures |
Source code |
Information Retrieval Data Structures & Algorithms |
Source code |
FIRE & SPARE |
C++ implementations of algorithms for finite automata, transducers, pattern matching of keywords and regular expressions |
{Codepage} |
listing of programming resources on the web |
Algorithms Archive |
maintained by Florian Schintke |
Illustrated Pattern Matching in Java |
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SAM |
Sequence Alignment and Modeling System |
Isearch |
software for indexing and searching text documents |
LPM and PAISLEI IDE |
Laleh's pattern matcher system for Win32 systems |
Icon Programming Language homepage |
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SNOBOL4 and SPITBOL Programming Languages |
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strmat package |
exact string matching and suffix trees |
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XPARAL: Graphical Computation of Parameterized Alignments |
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Graph Template Library |
GPL |
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string matching algorithm animation |
Smaa |
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nrgrep |
fast and flexible online pattern matching |
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Algorithm Archive |
by Scott Gasch (work in progress) |
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grappe |
pattern matching with wildcards |
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Boyer-Moore applet |
by Dieter Bühler |
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Aho-Corasick applet |
by Dieter Bühler |
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Naive, KMP, and BM pattern matching algorithms applet |
by Masayuki Takeda |
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Multi : Efficient Multi-Suffix-Tree String Dictionary |
by Stefan Edelkamp |
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Compact Affix Trees applet |
by Moritz G. Maaß |
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Suffix Trees applet |
by Moritz G. Maaß |
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Suffix Trees applet |
by Craig Nevill-Manning |
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Tree Structures for Algorithmic Problems on Strings |
suffix trees, suffix arrays software |
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ELAN |
a language where (equational) pattern matching plays a fundamental role |
Rewriting Calculus resources |
a calculus based on pattern matching |
A Library for Computational Biology Programs |
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A C++ regular expressions library |
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Sary: a suffix array library and tools |
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Sufary: a suffix array library |
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Boost Library |
Template C++ Library: contains Graph Library and RegEx++ Library |
CCP - a compact and fast algorithm for Regular Expression Search |
by J.-M. Champarnaud, F. Coulon, T. Paranthoen |
ANSI C implementation of a Suffix Tree |
by Dotan Tsadok, Shlomo Yona, Offer Kaye |
Suffix Arrays |
by M. Douglas McIlroy |
C Library to search over compressed texts |
by Paolo Ferragina, Alessandro Tommasi, Giovanni Manzini |
Linear-time and Lightweight Suffix Arrays construction |
by Juha Kärkkäinen |
PERL module String:Approx |
by Jarkko Hietaniemi |
TRE: regexp matching library |
by Ville Laurikari |
Regular expression (regex/grep) string matching |
by Nic Roets |
Yet another suffix tree implementation |
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MREPS |
tandem repeats |
YASS |
local aligment |
STR Library |
a fast C++ string class with RegExp |
Pizza&Chili Corpus |
Compressed Indexes and their Testbeds |
Tom |
pattern matching compiler for Java or C |
StringSearch |
pattern matching algorithms in Java (BMH, BMHR, BNDM and others) |
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News Groups and Mailing Lists |
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Theory-Edge |
theoretical computer science on Egroups |
comp.compression |
data compression |
comp.compression.research |
data compression research |
comp.theory.info-retrieval |
theory of information retrieval |
comp.theory |
theoretical computer science |
comp.text
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text processing |
comp.infosystems.harvest |
information systems harvest |