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Local alignment and BLAST. Usman Roshan BNFO 601. Local alignment. Global alignment recursions: Local alignment recursions. Local alignment traceback. Let T(i,j) be the traceback matrices and m and n be length of input sequences. Global alignment traceback:

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Local alignment and blast l.jpg

Local alignment and BLAST

Usman Roshan

BNFO 601


Local alignment l.jpg
Local alignment

  • Global alignment recursions:

  • Local alignment recursions


Local alignment traceback l.jpg
Local alignment traceback

  • Let T(i,j) be the traceback matrices and m and n be length of input sequences.

  • Global alignment traceback:

    • Begin from T(m,n) and stop at T(0,0).

  • Local alignment traceback:

    • Find i*,j* such that T(i*,j*) is the maximum over all T(i,j).

    • Begin traceback from T(i*,j*) and stop when

      T(i,j) <= 0.


Blast l.jpg
BLAST

  • Local pairwise alignment heuristic

  • Faster than standard pairwise alignment programs such as SSEARCH, but less sensitive.

  • Online server: http://www.ncbi.nlm.nih.gov/blast


Blast5 l.jpg
BLAST

  • Given a query q and a target sequence, find substrings of length k (k-mers) of score at least t --- also called hits. k is normally 3 to 5 for amino acids and 12 for nucleotides.

  • Extend each hit to a locally maximal segment. Terminate the extension when the reduction in score exceeds a pre-defined threshold

  • Report maximal segments above score S.


Finding k mers quickly l.jpg
Finding k-mers quickly

  • Preprocess the database of sequences:

    • For each sequence in the database store all k-mers in hash-table.

    • This takes linear time

  • Query sequence:

    • For each k-mer in the query sequence look up the hash table of the target to see if it exists

    • Also takes linear time