The best tutorial on HMMs

A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition (PDF)

GeneFinding

• Genscan: Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• EasyGene - a prokaryotic gene finder that ranks ORFs by statistical significance (PDF)
• SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model (PDF)
• Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• Integrating Genomic Homology into Gene Structure Prediction (PDF)
• Christopher Burge's PhD Thesis (PS) (PDF)

Sequence Alignment

• LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (PDF)
• Glocal Alignment: Finding Rearrangements During Alignment (PDF)
• AVID: A Global Alignment Program (PDF)
• BLAT: The BLAST-Like Local Alignment Tool (PDF)
• Gapped BLAST and PHI-BLAST (PDF)
• Pattern Hunter: Faster and more sensitive homology search (PDF)
• The estimation of statistical parameters for local alignment score distributions (PDF)
• T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment (PDF)

Fragment Assembly

• Genome Sizes (HTML)
• Transposons (HTML)
• Genomic mapping, mathematical analysis (PDF, PDF)
• ARACHNE: A Whole-Genome Shotgun Assembler (PDF)
• ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes (PDF)
• The Eulerian path approach to DNA fragment assembly (PDF)

Gene Regulation and Motif Finding

• Transcriptional Regulation of the Stem Cell Leukemia Gene (PDF)
• Exploring the conditional co-regulation of yeast gene expression through fuzzy k-means clustering (PDF)
• Systematic determination of genetic network architecture (PDF)
• Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences (PDF)
• Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment (PDF)

Conditional Random Fields

• CRF (PDF)
• Intro to CRF (PDF)