'Local alignments' presentation slideshows

Biology 224 Tom Peavy Sept 20 & 22, 2010

BLAST : Basic local alignment search tool. Biology 224 Tom Peavy Sept 20 & 22, 2010. Slides derived from Bioinformatics and Functional Genomics by Jonathan Pevsner>. BLAST. BLAST (Basic Local Alignment Search Tool) allows rapid sequence comparison of a query

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BLAST

BLAST. Getting the most from your cycles . Tom Madden NCBI/NLM/NIH madden@ncbi.nlm.nih.gov. The BLAST algorithm. What is BLAST?. B asic L ocal A lignment S earch T ool Calculates similarity for biological sequences.

1.1k views • 58 slides

BCB 444/544

BCB 444/544. Lecture 12 Multiple Sequence Alignment (MSA) PSSMs & Psi-BLAST #12_Sept17. Required Reading ( before lecture). ? Mon Sept 17 - Lecture 12 Position Specific Scoring Matrices & PSI-BLAST Chp 6 - pp 75-78 (but not HMMs)

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LSM2104 Part II Lectures 3 and 4

LSM2104 Part II Lectures 3 and 4. Tan Tin Wee Dept of Biochemistry NUS. Topics. Derivation of PAM and BLOSUM and Scoring Matrices Basic Introduction to Dynamic Programming Techniques Details of Needleman-Wunsch and Smith-Waterman Algoriths FASTA and BLAST Heuristics

674 views • 51 slides

August 26, 2011 Biochemistry 201 David Worthylake, 7152 MEB, x5176

Sequence Alignments and Database Searching. August 26, 2011 Biochemistry 201 David Worthylake, 7152 MEB, x5176. Protein A of interest to you. ornithine decarboxylase?. Why compare protein sequences?. Significant sequence similarities allow associations based upon known functions.

521 views • 42 slides

Multiple Sequence Alignments Advanced BLAST searches

Multiple Sequence Alignments Advanced BLAST searches. June 17, 2014. Topics. Overview of MSA MSA methods Practical aspects MSA to Profiles PSI- BLAST PHI-BLAST. Overview of MSA. Alignment of ? 3 sequences to bring as many similar characters into register as possible

1.41k views • 42 slides

Welcome to CS262!

Welcome to CS262!. Goals of this course. Introduction to Computational Biology Basic biology for computer scientists Breadth: mention many topics & applications In-depth coverage of Computational Genomics Algorithms for sequence analysis Current applications, trends, and open problems

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Sequence Alignment (Courtesy of Dr. S. Batzoglou )

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Multiple Sequence Alignments

Multiple Sequence Alignments. Progressive Alignment. x. When evolutionary tree is known: Align closest first, in the order of the tree In each step, align two sequences x, y, or profiles p x , p y , to generate a new alignment with associated profile p result Weighted version:

494 views • 38 slides

Dot Matrices Global Alignments Local Alignment

HOW Can we Align Two Sequences ?. Dot Matrices Global Alignments Local Alignment. Dot Matrices. QUESTION. What are the elements shared by two sequences ?. >Seq1 THEFATCAT >Seq2 THELASTCAT. T. H. E. F. A. T. C. A. T. T. Window. H. E. Stringency. F. A. S. T. C. A. T.

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Homework is at the end!!!!

Finding identities and similarities in nucleotide and protein sequences: What proteins are like mine? What the evolutionary history? Can I infer function of my gene/protein?. Homework is at the end!!!!. Overview. Similarity vs homology Orthologs and paralogs

1.13k views • 33 slides

Multiple Sequence Alignments

Multiple Sequence Alignments. Progressive Alignment. x. When evolutionary tree is known: Align closest first, in the order of the tree In each step, align two sequences x, y, or profiles p x , p y , to generate a new alignment with associated profile p result Weighted version:

568 views • 33 slides

Inference of Allele Specific Isoform Expression (ASIE) Levels from RNA- Seq Data

Inference of Allele Specific Isoform Expression (ASIE) Levels from RNA- Seq Data. Sahar Al Seesi and Ion M ? ndoiu Computer Science and Engineering CANGS 2012. Outline. Problem definition Challenges and limitations of current approaches ASIE pipeline SNVQ RefHap Diploid IsoEM

651 views • 33 slides

Large-Scale Global Alignments Multiple Alignments

Large-Scale Global Alignments Multiple Alignments. Lecture 10, Thursday May 1, 2003. ARACHNE: Steps to Assemble a Genome. 1. Find overlapping reads. 2. Merge good pairs of reads into longer contigs. 3. Link contigs to form supercontigs. 4. Derive consensus sequence.

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Real-world protein aligners

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Roadmap

Roadmap. The topics: basic concepts of molecular biology more on Perl overview of the field biological databases and database searching sequence alignments phylogenetics structure prediction microarray data analysis. Sequence alignments. Introduction What is an alignment?

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Multiple Sequence Alignment

386 views • 18 slides

Sequence Alignment Examples

Sequence Alignment Examples. Fall 2003 Dr. Susan Bridges. Global Alignment Example. Different scoring functions can be used with any of the algorithms. For this example, use the following scoring function: Indel (add a space) -2 Match +2 Substitution -1. Global Alignment Result.

336 views • 17 slides

Sequence Alignment

Sequence Alignment. Kun-Mao Chao ( ??? ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan E-mail: kmchao@csie.ntu.edu.tw WWW: http://www.csie.ntu.edu.tw/~kmchao. k best local alignments.

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LAGAN and MLAGAN

291 views • 13 slides