'Profile alignment' diaporamas de présentation

1-month Practical Course Genome Analysis Lecture 5: Multiple Sequence Alignment

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. 1-month Practical Course Genome Analysis Lecture 5: Multiple Sequence Alignment Centre for Integrative Bioinformatics VU (IBIVU)

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Building synteny maps

Building synteny maps. Recommended local aligners BLASTZ Most accurate, especially for genes Chains local alignments WU-BLAST Good tradeoff of efficiency/sensitivity Best command-line options BLAT Fast, less sensitive Good for comparing very similar sequences

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Molecular Replacement

Molecular Replacement Martyn Winn CCP4 group, Daresbury Laboratory, UK What do we know from the diffraction data? The point group of the new crystal form, the volume of the asymmetric unit and hence the likely number of molecules it contains (Matthews coefficient).

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Multiple sequence alignment methods

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Some new sequencing technologies

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Sequence analysis course

Sequence analysis course. Lecture 6 Multiple sequence alignment 2 of 3 Multiple alignment methods. Biological definitions for related sequences.

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Introduction to bioinformatics Lecture 8 Multiple sequence alignment (2)

Introduction to bioinformatics Lecture 8 Multiple sequence alignment (2). Flavodoxin-cheY: Pre-processing (prepro 1500). Progressive multiple alignment general principles. 1. Score 1-2. 2. 1. Score 1-3. 3. 4. Score 4-5. 5. Scores. Similarity matrix. 5×5. Scores to distances.

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Ch6 multiple sequence alignment methods

Ch6 multiple sequence alignment methods. Biologists produce high quality multiple sequence alignment by hand using knowledge of protein sequence evolution. Automatic multiple sequence alignment? -in probabilistic modeling, scoring function is primary concern, not the alignment algorithm. 1.

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Class 5: Multiple Sequence Alignment

Class 5: Multiple Sequence Alignment. Multiple sequence alignment. VTISCTGSSSNIGAG-NHVKWYQQLPG VTISCTGTSSNIGS--ITVNWYQQLPG LRLSCSSSGFIFSS--YAMYWVRQAPG LSLTCTVSGTSFDD--YYSTWVRQPPG PEVTCVVVDVSHEDPQVKFNWYVDG-- ATLVCLISDFYPGA--VTVAWKADS-- AALGCLVKDYFPEP--VTVSWNSG---

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Multiple Sequence Alignment

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Home Work

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1-month Practical Course Genome Analysis 2008 Lecture 3: Profiles: representing sequence alignment

C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. 1-month Practical Course Genome Analysis 2008 Lecture 3: Profiles: representing sequence alignment Centre for Integrative Bioinformatics VU (IBIVU)

328 views • 13 slides