'Affine gap' presentation slideshows

Bioinformatics

Bioinformatics. Pairwise alignment Revised 26/02/10. III. I. II. Introduction. Why aligning sequences? Functional inference Clone and sequence gene with unknown function Aligning sequence with other sequence in databank detect homologues with known function Ortholog, paralog

911 views • 75 slides

NCBI Molecular Biology Resources

836 views • 71 slides

Multiple Sequence Alignment

Multiple Sequence Alignment. Alexei Drummond. Week 3 Learning Outcomes. Be able to compute the Smith-Waterman (local) pairwise alignment of two sequences given a score matrix and gap penalty

775 views • 67 slides

Bioinformatics

Bioinformatics. Pairwise alignment Revised 0/12/06. III. I. II. Introduction. Why aligning sequences? Functional inference Clone and sequence gene with unknown function Aligning sequence with other sequence in databank detect homologues with known function Ortholog, paralog

1.06k views • 64 slides

Pair-wise 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. Introduction to bioinformatics 2007 Lecture 5. Pair-wise Sequence Alignment. Bioinformatics.

782 views • 61 slides

Sequence Alignment

Sequence Alignment. Kun-Mao Chao ( ??? ) Department of Computer Science and Information Engineering National Taiwan University, Taiwan WWW: http://www.csie.ntu.edu.tw/~kmchao. Useful Websites. MIT Biology Hypertextbook http://www.mit.edu:8001/afs/athena/course/other/esgbio/www/7001main.html

553 views • 45 slides

Database Searching:BLAST and FASTA

Database Searching:BLAST and FASTA. Biological Sequence Databases. NCBI Nucleotide GenBank, EMBL, DDBJ, GSDB, patent sequences Protein SwissProt, PIR, PRF, PDB (structural) PopSet GDB, FlyBase, OMIM, HGMD, MGD, GED There are other types of biological databases : EcoCyc, WIT/WIT2, others.

771 views • 44 slides

Barking Up the Wrong Treelength

Kevin Liu, Serita Nelesen, Sindhu Raghavan, C. Randal Linder, and Tandy Warnow IEEE TCCB 2009. Barking Up the Wrong Treelength. Minimizing Treelength. Generalized Input: set S of sequences and a function f(s, s') for the edit distance between sequences s and s'

412 views • 33 slides

Comp. Genomics

Comp. Genomics. Recitation 2 12/3/09 Slides by Igor Ulitsky. Outline. Alignment re-cap End-space free alignment Affine gap alignment algorithm and proof Bounded gap/spaces alignments. Dynamic programming. Useful in many string-related settings Will be repeatedly used in the course

405 views • 29 slides

Developing Pairwise Sequence Alignment Algorithms

Developing Pairwise Sequence Alignment Algorithms. Dr. Nancy Warter-Perez. Outline. Group assignments for project Overview of global and local alignment References for sequence alignment algorithms Discussion of Needleman-Wunsch iterative approach to global alignment

469 views • 27 slides

Comp. Genomics

Comp. Genomics. Recitation 1. Outline. Sequence alignment End-space free alignment Alignment with gaps. x i | G. y j | C. Alignment basic step. x i |G. y j |C. G. C. x i |G. y j |C. G. -. x i |G. -. y j |C. C. Global alignment. All of x has to be aligned with all of y

460 views • 27 slides

Sequence Alignment

Sequence Alignment. Motivation: Types. Two sequences of same length, some characters are different ( Database search) Aagtacggaga aagcaccgaga Two seq are of different length, possible gaps in one of them ( Database search) Aaccaccgaga Aa-caccgaga. Motivation: Types.

409 views • 25 slides

Sequence Alignment

Sequence Alignment. Motivation: Types. Two sequences of same length, some characters are different ( Database search) Aagtacggaga aagcaccgaga Two seq are of different length, possible gaps in one of them ( Database search) Aaccaccgaga Aa-caccgaga. Motivation: Types.

266 views • 25 slides

Global Alignment Summary

Global Alignment Summary. If Score(i, j) denotes best score to aligning A[1 : i] and B[1 : j] Score(i-1, j) + g align A[i] with GAP Score(i, j-1) + g align B[j] with GAP Score( i , j) = max Score(i-1, j-1) + m if A[i] == B[j ]

389 views • 20 slides

Sequence comparison: Introduction and motivation

Sequence comparison: Introduction and motivation. Genome 559: Introduction to Statistical and Computational Genomics Prof. William Stafford Noble. Logistics. Syllabus Should I take this class?. BioPics. Please enroll in BioPics on your computer. Motivation.

298 views • 19 slides

Developing Sequence Alignment Algorithms in C++

Developing Sequence Alignment Algorithms in C++. Dr. Nancy Warter-Perez May 21, 2002. Outline. Hand out project Group assignments References for sequence alignment algorithms Board example of Needleman-Wunch

274 views • 15 slides