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# Local alignment and BLAST - PowerPoint PPT Presentation

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

Usman Roshan

BNFO 601

• Global alignment recursions:

• Local alignment recursions

• 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.

• 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

• 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.

• 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