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LU3: Sequence Analysis (Pairwise Alignment (BLAST Programming (Matching…

- - - - "Word" - a segment of sequences of pre-determined length (10 nt for a DNA of 3 aa for protein)
      - "Word hit" - consists of a pair of very similar words from each of the sequences (query and subject)
        
        for DNA sequences - words must be identical
        
        for protein sequences - must be highly similar
      - During alignment each word is extended in both directions without introducing gaps.
    - - Reported alignments are those with the overall highest scores
      - High-scoring segment pairs (HSPs) - word hits with a high score (high similarity)
        
        best HSP - extended by extending the alignment in both directions
        
        extension continues until the end of the sequence, or until the alignment becomes illogical
- - - - CLUSTAL (W & X)
      - SEQUENCHER
        
        DNA analysis software that has multiple alignment capabilities
        
        based on an optimized version of the Smith-Waterman algorithm (Progressive Pairwise Method) that improves the speed and accuracy of data analysis
        
        Functions:
        
        provides tools for viewing, editing, and assembling of data generated by automated DNA sequencers on the desktop computer
        
        recalculates alignment en masse or en bloc with new dataset addition
        
        handles (import and export) a variety of data formats
        
        import files directly from almost all automated DNA sequencing systems
        
        Features:
        
        Import and store raw sequence data
        
        Displays alignment of DNA sequences and their associated chromatograms in a single window
        
        Applicable for Contig mapping and generation of composite data (derived sequences)
        
        A consensus sequence is an ideal representation of acceptable template for referencing
      - PILEUP
        
        Multiple alignment program in the GCG package
        
        Processes:
        
        calculate approximate pairwise similarity scores between all sequences to be aligned, and they are clustered into a dendrogram (tree structure)
        
        most similar pairs of sequences are aligned
        
        new sequences and clusters of sequences are added one by one, according to the branching order in the dendrogram
        
        since the alignment is calculated on a progressive basis, the order of the initial sequences can affect the final alignment
        
        takes quite a while to align more than about 10 sequences
        
        editing can be done by using LINEUP
    - - MAP
      - ITERALIGN
      - MultAlin