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Pairwise Sequence Alignment JASMIN SUTKOVIC FALL 2019
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 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 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. .
Setup is the key for good results. . .
Some other websites relevant to bioinformatics. . . Swiss Prot http: //www. expasy. org/ PDB – Protein Data Bank http: //www. rcsb. org/