'Gapped alignment' presentation slideshows

Gapped BLAST and PSI-BLAST ? a new generation of protein database search programs

Gapped BLAST and PSI-BLAST ? a new generation of protein database search programs. Presented by ??? ??? ??? ???. Outline. BLAST 1.0 BLAST 2.0 The two-hit method Gapped alignment PSI-BLAST Performance evaluation Discussion and Conclusion NCBI website. Statistical preliminaries.

866 views • 86 slides

Introduction to the theory of sequence alignment

Introduction to the theory of sequence alignment. Yves Moreau Master of Artificial Intelligence Katholieke Universiteit Leuven 2003-2004. References.

467 views • 38 slides

Introduction to the theory of sequence alignment

Introduction to the theory of sequence alignment. Yves Moreau Master of Artificial Intelligence Katholieke Universiteit Leuven 2003-2004. References.

384 views • 38 slides

Last lecture summary

590 views • 33 slides

Bioinformatics Part 3: Pairwise Alignments and Database Searches

Bioinformatics Part 3: Pairwise Alignments and Database Searches. Similarity, homology and identity Gap penalties and scoring matrices in pairwise alignments Alignment algorithms Database searching: BLAST and FASTA. Similarity, Homology and Identity.

291 views • 18 slides

Class 5: HMMs and Profile HMMs

Class 5: HMMs and Profile HMMs. Review of HMM. Hidden Markov Models Probabilistic models of sequences Consist of two parts: Hidden states These act like a stochastic automata Observations These are determined (stochastically) by the hidden state. 0.95. 0.9. 1: 1/10 2: 1/10 3: 1/10

234 views • 11 slides

Heuristic homology search methods

Heuristic homology search methods. Heuristic methods. Heuristic methods make 'reasonable assumptions' about the nature of the sequence alignments. This allows them to cut corners by trying out only the most likely alignments. The benefit is that they run MUCH faster than an exhaustive search.

213 views • 6 slides

Protein structure prediction

218 views • 4 slides

Read

Incorrect mapping (non-gapped alignment). GTXX. r. e1. e2. GTXX. GTXX. AG GTXX. GTXX. r. C orrect mapping (spliced alignment). (1 ) Read r may be incorrectly mapped to the intron between exons e1 and e2 . e1. e2. e3. Gene. Read. m apped. e1. e2. e3. Processed pseudogene.

186 views • 1 slides