• Protein Family-based Methods for Homology Detection & Analysis Higgins&Talyor Ch5 (Overview) PDF
  • Patterns and regular expressions for analysis of biological sequences Björn Olsson, PDF
  • Protein Families, secondary databases Amir Mitchell PPT
  • Protein Families and Gene Ontology PPT
  • Variations on probabilistic suffix trees: statistical modeling and prediction of protein families Gill Bejerano and Golan Yona
  • Using substitution probabilities to improve position-specific scoring matrices Jorja G. Henikoff and Steven Henikoff, PDF
  • Position-based sequence weights Steven Henikoff1 and Jorja G. Henikoff, PDF
  • Patterns, profiles and multiple sequence alignment
  • Protein Family Classification using Sparse Markov Transducers, PPT
  • MISAE: A New Approach for Regulatory Motif Extraction. Zhaohui Sun, Jingyi Yang, Jitender S. Deogun, PDF
  • Local Prediction Approach for Protein Classification Using Probabilistic Suffix Trees Zhaohui Sun Jitender S. Deogun, PDF
  • Domains, motifs, and clusters in the protein universe Jinfeng Liu, Burkhard Rost, PDF
  • DIMACS Workshop on Integration of Diverse Biological Data
  • Pattern Discovery from Biosequences, PDF
  • Sequence Alignment Methods: Dynamic Programming and Heuristic Approaches. Jaroslaw Meller, PPT
  • HIDDEN MARKOV MODELS
  • A set reduction and pattern matching problem motivated by Allele Specific Primer Design Christopher T Lewis, PDF
  • Motif Search Irit Orr, PDF
  • Sequence Patterns, Domains, Profiles & HMMs Frank J. Lebeda, PDF
  • Multiple alignments
  • Introduction to Profiles and Hidden Markov Models, PDF
  • Protein family alignment annotation, PDF
  • Profile Analysis,John Devereux
  • Motif search help page
  • Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database V. S. Gowri, Shashi B. Pandit, P. S. Karthik, N. Srinivasan and S. Balaji
  • Protein family classification using sparse Markov transducers Eleazar Eskin, William Stafford Noble and Yoram Singer
  • Modeling protein families using probabilistic suffix trees
  • A comparison of position-specific score matrices based on sequence and structure alignments Anna R. Panchenko and Stephen H. Bryant
  • Functional classification of proteins by pattern discovery and top-down clustering of primary sequences by A. H. Liu and A. Califano
  • Alignment of protein sequences by their profiles MARC A. MARTI-RENOM, M.S. MADHUSUDHAN, AND ANDREJ SALI, PDF
  • Blocks, Profiles & Blocks, Profiles & Hidden Markov Hidden Markov Models Doug Brutlag & Lee Doug Brutlag & Lee Kozar, PDF
  • Discovering Active Motifs in Sets of Related Protein Sequences and Using Them for Classification Jason T. L. Wang Thomas G. Marry Dennis Shashaz Bruce Shapiro Gung-Wei Chirn, PDF
  • Hidden Markov Models with Bioinformatics Applications,Nanwei Cao, PDF
  • An Introduction to Hidden Markov Models for Biological Sequences by Anders Krogh, PDF
  • Patterns, profiles and multiple sequence align
  • Searching sequence databases using protein family-based methods Torbjørn Rognes, PPT
  • Motifs and Signals in Protein Sequences, PDF
  • Patterns, profiles David Gilbert, PDF
  • Study of Motif Correlation in Proteins by Data Mining, PDF
  • Protein Classification and Meta-organization. Methods for Global Organization of the Protein Universe, Golan Yona PPT
  • REGULAR EXPRESSIONS
  • Motifs and Profile Analysis, Mona Singh, PDF
  • Protein Family Classification using Sparse Markov Transducers Eleazar Eskin William Stafford Noble Yoram Singer, PDF
  • PROTEIN PATTERN DATABASES, PDF
  • Profile HMMs for protein searches and other applications
  • Regular Expression for Protein Motif Search
  • Regular Expression for Protein Motif Search
  • Profile Analysis Marina Alexandersson, PDF
  • The role of pattern databases in sequence analysis Terri K. Attwood PDF
  • Protein Pattern and Domain Databases
  • Modeling protein families, PDF
  • Patterns in biosequences
  • Improved smoothing for Probabilistic Suffix Trees seen as variable order Markov chains Christopher Kermorvant, PDF
  • Benefits of a Generalized Profile Syntax for Biomolecular Sequence Motifs Kay Hofmann and Philipp Bucher
  • Methods for the construction of profile entries for the PROSITE database Kay Hofmann and Philipp Bucher
  • Weak Homology Detection by Profile-Profile Comparison, PDF
  • PROTEIN CLUSTERING AND CLASSIFICATION ori Sasson and Michal Linial PDF
  • Sequence Patterns and Transcriptional Regulation Timothy L. Bailey, PPT
  • Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bejerano G, Yona G
  • Use of motifs in sequence analysis
  • Protein Pattern, Motif, and Domain Databases
  • Protein Pattern, Motif, and Domain Databases
  • Tools and resources for identifying protein families, domains and motifs Nicola J. Mulder1 and Rolf Apweiler
  • Systematic and Automated Discovery of Patterns in PROSITE Families Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, and Andrea Califano, PDF
  • Lecture in Multiple Sequence Alignments
  • PROSITE patterns and rules
  • Sequence analysis: Macromolecular motif recognition, Sylvia Nagl, PPT
  • Protein Family Classifiction using Sparse Markov Transducers
  • Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences Eleazar Eskinyand William Noble Grundy Yoram Singer, PDF
  • Motifs and patterns David Gestel
  • HMMER: profile HMMs for protein sequence analysis