Pairwise Sequence Alignment JASMIN SUTKOVIC FALL 2019 Homology

  • Slides: 31
Download presentation
Pairwise Sequence Alignment JASMIN SUTKOVIC FALL 2019

Pairwise Sequence Alignment JASMIN SUTKOVIC FALL 2019

Homology Orthologs Divergence follows speciation A gene from common ancestor is found (has duplicated)

Homology Orthologs Divergence follows speciation A gene from common ancestor is found (has duplicated) in two different species Paralogs Divergence follows duplication A gene has duplicated within the same species “Para” in Greek - side by side

Alignment Types Global (Needleman & Wunsch) Local (Smith & Waterman) Semi-global (Glocal) It is

Alignment Types Global (Needleman & Wunsch) Local (Smith & Waterman) Semi-global (Glocal) It is like a global alignment, but spaces at the beginning and/or end of an alignment are ignored

Alignment Tools BLAST Basic Local Alignment Search Tool Alignments contain short lengths of exact

Alignment Tools BLAST Basic Local Alignment Search Tool Alignments contain short lengths of exact matches FASTA Fast All Originally FASTP (only for protein) Later on for “All” (DNA and protein) Blast vs Fasta Blast is much faster than Fasta. Blast is much more accurate than Fasta. For closely matched sequences Blast is very accurate and for dissimilar sequence Fasta is better software. Blast can be modified according to the need but Fasta cannot be modified. Blast has to use Fasta input format to get the output data. Blast is much more versatile and widely used than Fasta.

NCBI guys. .

NCBI guys. .

Setup is the key for good results. . .

Setup is the key for good results. . .

Some other websites relevant to bioinformatics. . . Swiss Prot http: //www. expasy. org/

Some other websites relevant to bioinformatics. . . Swiss Prot http: //www. expasy. org/ PDB – Protein Data Bank http: //www. rcsb. org/

Pairwise Sequence Alignment JASMIN SUTKOVIC 18 10 2018Pairwise Sequence Alignment JASMIN SUTKOVIC 18 10 2018
Pairwise sequence Alignment Sequence Alignment Sequence analysis isPairwise sequence Alignment Sequence Alignment Sequence analysis is
Multiple Sequence Alignment Multiple Alignment versus Pairwise AlignmentMultiple Sequence Alignment Multiple Alignment versus Pairwise Alignment
Pairwise sequence Alignment Types of Alignment Global alignmentPairwise sequence Alignment Types of Alignment Global alignment
bioinformatics Bioinformatics Sequence alignment Pairwise Alignment Sequence Abioinformatics Bioinformatics Sequence alignment Pairwise Alignment Sequence A
Exercises Pairwise alignment Homology search BLAST Multiple alignmentExercises Pairwise alignment Homology search BLAST Multiple alignment
Exercises Pairwise alignment Homology search BLAST Multiple alignmentExercises Pairwise alignment Homology search BLAST Multiple alignment
Homology and sequence alignment 1 Homology Similarity betweenHomology and sequence alignment 1 Homology Similarity between
Pairwise Sequence Alignment Pairwise alignments in the 1950Pairwise Sequence Alignment Pairwise alignments in the 1950
Homology and Cladistics Homology Homology a shared traitHomology and Cladistics Homology Homology a shared trait
Homology versus Analogy Evolutionary Homology Serial Homology CriteriaHomology versus Analogy Evolutionary Homology Serial Homology Criteria
BNFO 136 Sequence alignment Usman Roshan Pairwise alignmentBNFO 136 Sequence alignment Usman Roshan Pairwise alignment
GA for Sequence Alignment Pairwise alignment Multiple stringGA for Sequence Alignment Pairwise alignment Multiple string
Sequence alignment with NeedlemanWunsch Usman Roshan Pairwise alignmentSequence alignment with NeedlemanWunsch Usman Roshan Pairwise alignment
BNFO 136 Sequence alignment Usman Roshan Pairwise alignmentBNFO 136 Sequence alignment Usman Roshan Pairwise alignment
Pairwise Sequence Alignment LESSON 3 1 Alignment lPairwise Sequence Alignment LESSON 3 1 Alignment l
COMP 571 Bioinformatics Sequence Analysis Pairwise Sequence AlignmentCOMP 571 Bioinformatics Sequence Analysis Pairwise Sequence Alignment
Homology and Homologs Homology just means sequence similarityHomology and Homologs Homology just means sequence similarity
n Sequence homology similarity and comparison Homology isn Sequence homology similarity and comparison Homology is
A Subquadratic Sequence Alignment Algorithm Global alignment AlignmentA Subquadratic Sequence Alignment Algorithm Global alignment Alignment
Computational Molecular Biology Multiple Sequence Alignment Sequence AlignmentComputational Molecular Biology Multiple Sequence Alignment Sequence Alignment
Class 5 Multiple Sequence Alignment Multiple sequence alignmentClass 5 Multiple Sequence Alignment Multiple sequence alignment
Sequence Alignment Two general methods for sequence alignmentSequence Alignment Two general methods for sequence alignment
Lecture 4 Sequence alignment and searching Sequence alignmentLecture 4 Sequence alignment and searching Sequence alignment