1. Pairwise Sequence Alignment
Jasmin sutkovic, – bioinformatics lab 2

2. Homology Orthologs Paralogs “Para” in Greek - side by side
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
Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Orthologs retain the same function in the course of evolution
Paralogs are genes related by duplication within a genome, paralogs evolve new functions, even if these are related to the original one.

3. 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
Semi-global alignment bioinformatics applications
Ignoring flanking (starting or trailing) spacing may be desirable in some situations.
Prokaryotes: aligning genes.
Eukaryotes: aligning an exon to the original gene sequence; spaces adjacent to the exon may be due to an untranslated region or introns.
Sequence assembly: ignore starting spaces of the first sequence and trailing spaces of the second sequence.

4. Alignment Tools Blast vs Fasta BLAST 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.
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)

5. NCBI guys....

30. Setup is the key for good results...

31. Some other websites relevant to bioinformatics...
Swiss Prot
PDB – Protein Data Bank