| 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, Søren 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 |
| 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 |
NEW |
| 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 |
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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
|
text processing |
| comp.infosystems.harvest |
information systems harvest |