multiple sequence alignment

Multiple sequence alignment

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Multiple sequence alignment

Uses

•Pair-wise sequence alignment, Multiple sequence alignment Evolutionary relationships

•Multiple sequence alignment Information structural relationships Information on the most alike regionsPrediction of specific probes

Relationship b/w msa & Evolutionary tree construction

As an extension of sequence pair alignment by

Dynamic programming

Alignment of 3 sequences by DP

Alignment of 3 sequences by DP

Scoring gap penalties by the MSA

Natural gap cost: The sum of the no. of gaps in all pair-wise combinations

Quasi-natural gap cost: Natural cost + additional value for any gap that begins and ends within another

SP model for scoringa msa

Progressive alignment

CLUSTALW

CLUSTALW

CLUSTALW

Multiple Sequence Alignment

Multiple Sequence Alignment - CBCB · • A multiple sequence alignment (MSA) implies a pairwise alignment between every pair of sequences. ... • Multiple sequence alignments (MSAs)

Creating Multiple Sequence Alignments - Plant … · Web viewSequence Alignment, Multiple Sequence Alignment and Phylogenetics Copy 10_Lab3 from Z: to C:. A. SEQUENCE ALIGNMENT The

Lecture 5: Multiple sequence alignment · Lecture 5: Multiple sequence alignment Introduction to Computational Biology Teresa Przytycka, PhD . Why do we need multiple sequence alignment

Protein Multiple Sequence Alignment

Fast Sequence Search Multiple Sequence Alignment

1 Multiple sequence alignment Lesson 3. 2 1. What is a multiple sequence alignment?

3.4 Multiple sequence alignment and domain findingibi.zju.edu.cn/.../Bioinformatics/multiple_align_03... · (1) Multiple sequence alignment and progressive global alignment (ClustalW)

Multiple Sequence Alignment (I)

Multiple sequence alignment MSA

RNA multiple sequence alignment

Local Multiple Sequence Alignment Sequence Motifs

Multiple Sequence Alignment (II)

Basics of Multiple Sequence Alignment - Tandy Warnowtandy.cs.illinois.edu/msa-basics.pdf · A multiple sequence alignment 220 Multiple sequence alignment P1 a1 - a2 a3 a4 a5 P2 b1

Multiple Sequence Alignmentckingsf/bioinfo-lectures/msa.pdf · Multiple Sequence Alignment (MSA) Multiple sequence alignment: ﬁnd more subtle patterns & ﬁnd common patterns between

Multiple sequence alignment Why?

W: multiple sequence alignment through sequence weighting ...homes.di.unimi.it/valenti/SlideCorsi/.../allineamento.multiplo.2.pdf · multiple sequence alignment through sequence weighting,

Protein Sequence Alignment Multiple Sequence Alignment

Multiple Sequence Composition Alignment

Part II : Sequence Comparison Multiple Sequence Alignment

Multiple Sequence Alignment - FASTA Multiple Sequence Alignment Goals of today’s lecture: • Why multiple sequence alignment (MSA)? –identify conserved (functional?) positions

Lecture 5: Multiple sequence alignment€¦ · Refining multiple sequence alignment • Given – multiple alignment of sequences • Goal improve the alignment • One of several

Local Multiple Sequence Alignment Sequence Motifs

Multiple sequence alignment · 10/11/2006 · Multiple sequence alignment: today’s goals • to define what a multiple sequence alignment is and how it is generated; to describe

Multiple Sequence Alignment (MSA)

multiple sequence alignment

Education

msanatural gap cost

dynamic programming

dpscoring gap penalties

sp model