Please enable JavaScript.

Coggle requires JavaScript to display documents.

BLAST, BLAST - Coggle Diagram

- - - - Low complexity = small repeating regions (like trimers), high A-T regions, etc.
      - Matches within these regions are not significant and can be misleading. Hence they are replaced by lowercase letters, when masked
      - RepeatMasker
        
        Screens DNA sequences against library of repeat elements.
        
        Can optionally also mask low complexity regions
        
        OUTPUT - detailed annotation of location of repeats and low complexity regions
        
        Can accidentally mask a region of interest
    - - MultiFasta file
      - Database scan
        
        Find exact matches/seed hit
        
        of 11 bases default for BLASTN
        
        of 28 bases default for MegaBLAST
        
        Faster and more sensitive than BLASTN, but less specific
        
        of 3 residues default for BLASTX/TBLASTN/BLASTP
        
        Extension from seed
        
        Gap-free extension - Thresholded
        
        Produces high scoring segment pairs (HSPs)
        
        Gapped extension - Smith Waterman
        
        Verify using Smith Waterman Local Alignment
        
        Evaluate using E values (default cutoff of 10)
        
        Can reduce if using large databases
        
        E value - expected number of hits with at least this score, against any database of this size.
        
        Other results
        
        2 more items...
        
        Extends local alignment in both directions to find best match around the seeds.
        
        Seeding - First finds high scoring matches between query Kmers (exact and similar) (length 11 for DNA and 3 for protein) and database sequences.
        
        Few small queries can be searched for in many large database sequences
      - Can create using command line
      - Important to select curated databases with up to date sequence information, to reduce redundant searching
- - - - Values in the matrix represent the likelihood of the AA of that row being substituted through one or more PAMs with the AA in that column for a given evolutionary interval, as opposed to alignment by chance
        
        % positives - percent of alignment positions that have a positive score in the substitution matrix
      - PAM40 - for short evolutionary time, strong local similarities
      - PAM120 - midrange
      - PAM250 - for long evolutionary interval, long and weak similarities
    - - Constructed by aligning protein sequences at set similarity (62%, 80%, etc.)
      - Long odds score - ratio of number of occurences of each AA combination in the observed data to the E value of occurrence of the pair in the alignment results
      - BLOSUM45 - distantly related
      - BLOSUM62 - midrange, default for BLASTP
      - BLOSUM80 - strongly related
      - Positive values in the substitution matrix - stronger is the relationship between the pair - reflected by the number of positives in a protein alignment results (for pairwise alignment)
- - - - Because of more seed alignments