The best tutorial on HMMs
A Tutorial on Hidden Markov Models and Selected Applications in Speech
Recognition: http://www.cs.berkeley.ed
GeneFinding
Sequence Alignment
Fragment Assembly
Gene Regulation and Motif Finding
Conditional Random Fields
A Tutorial on Hidden Markov Models and Selected Applications in Speech
Recognition: http://www.cs.berkeley.ed
GeneFinding
- Genscan: Prediction of Complete Gene Structures in Human Genomic DNA
http://ai.stanford.edu/%7Eserafi... - EasyGene - a prokaryotic gene finder that ranks ORFs by statistical
significance http://ai.stanford.edu/%7Eserafi... - SLAM - Cross-species Gene Finding and Alignment with a Generalized
Pair Hidden Markov Model http://ai.stanford.edu/%7Eserafi... - Prediction of Complete Gene Structures in Human Genomic DNAhttp://www.idealibrary.co
m/links... - Integrating Genomic Homology into Gene Structure Prediction
http://ai.stanford.edu/%7Eserafi... - Christopher Burge's PhD Thesis http://genes.mit.edu/burg
elab/Th...
Sequence Alignment
- LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
http://ai.stanford.edu/%7Eserafi... - Glocal Alignment: Finding Rearrangements During Alignment
http://ai.stanford.edu/%7Eserafi... - AVID: A Global Alignment Program
http://ai.stanford.edu/%7Eserafi... - BLAT: The BLAST-Like Local Alignment Tool
http://ai.stanford.edu/%7Eserafi... - Gapped BLAST and PHI-BLAST
http://ai.stanford.edu/%7Eserafi... - Pattern Hunter: Faster and more sensitive homology search
http://ai.stanford.edu/%7Eserafi... - The estimation of statistical parameters for local alignment score distributions
http://ai.stanford.edu/%7Eserafi... - T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment
http://ai.stanford.edu/%7Eserafi...
Fragment Assembly
- DOGS - Database Of Genome Sizes http://www.cbs.dtu.dk/dat
abases/... - Transposons: Mobile DNA http://www.ultranet.com/%
7Ejkimb... - Genomic Mapping by End-Characterized Random Clones, a mathematical analysis http://ai.stanford.edu/%7
Eserafi... - Sequencing a Genome by Walking with Clone-End
Sequences: A Mathematical Analysis http://ai.stanford.edu/%7Eserafi...
- ARACHNE: A Whole-Genome Shotgun Assembler
http://ai.stanford.edu/%7Eserafi... - ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes
http://ai.stanford.edu/%7Eserafi... - The Eulerian path approach to DNA fragment assembly
http://ai.stanford.edu/%7Eserafi...
Gene Regulation and Motif Finding
- Transcriptional Regulation of the Stem Cell Leukemia Gene
http://ai.stanford.edu/%7Eserafi... - Exploring the conditional co-regulation of yeast gene expression
through fuzzy k-means clustering http://ai.stanford.edu/%7Eserafi... - Systematic determination of genetic network architecture
http://ai.stanford.edu/%7Eserafi... - Identifying DNA and Protein Patterns with Statistically Significant
Alignments of Multiple Sequences http://ai.stanford.edu/%7Eserafi... - Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for
Multiple Alignment http://ai.stanford.edu/%7Eserafi...
Conditional Random Fields
- Semi-Markov Conditional Random Fields for
Information Extraction
http://ai.stanford.edu/%7Eserafi... - Conditional Random Fields: An Introduction
http://ai.stanford.edu/%7Eserafi...
