| Calling Sequence | DynProgScore(seq1,seq2,dm,modif)
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| Parameters |
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| Return Type | {[Score:numeric],[score:numeric, from1..to1, from2..to2]} | ||||||||||||||||||
| Synopsis | Computes the optimal cost of the alignment between seq1 and seq2 using the Dayhoff matrix dm, a specified alignment mode and a specified deletion cost model. It returns a triplet: [ Score, from1..to1, from2..to2 ] or [ Score ] where Score is the optimal score of the alignment and seq1[from1..to1] and seq2[from2..to2] are the selected portions of the sequences to align. seq1 and seq2 can be either peptide sequences, nucleotide sequences or probabilistic sequences, ProbSeq(). Modif is a set of strings which have the following meanings: | ||||||||||||||||||
For the alignment type, one of the following can be specified: | |||||||||||||||||||
Local - (default) a local alignment, the subsequences of seq1 and seq2 which give the highest score. | |||||||||||||||||||
Global - a global alignment, the entire seq1 is matched against the entire seq2. | |||||||||||||||||||
CFE - cost-free ends, the entire seq1 is matched against seq2, but one deletion at the ends is not penalized. | |||||||||||||||||||
CFEright - cost-free ends, the entire seq1 is matched against seq2, but one deletion at the right end is not penalized. | |||||||||||||||||||
Shake - align seq1 and seq2 up to the point where the maximum score happens. Then do the same backwards and forwards until no improvements of the score happen. | |||||||||||||||||||
MinLength(k) - align seq1 and seq2 as in a Local alignment (starting anyplace, ending anyplace) but at least k amino acids of each sequence are aligned. I.e. the minimum of the aligned lengths is k or larger. | |||||||||||||||||||
For the deletion cost model, one of the following can be specified: | |||||||||||||||||||
Affine - (default) deletion cost of a gap of length k is FixedDel + IncDel*(k-1). The values for FixedDel and IncDel are taken from the Dayhoff matrix dm. | |||||||||||||||||||
LogDel - logarithmic deletion cost, the cost of a gap of length k is DelFixedLog + DelLog*log(k). The values for DelFixedLog and DelLog are taken from the Dayhoff matrix dm. | |||||||||||||||||||
For the type of result, any combination of the following can be specified: | |||||||||||||||||||
JustScore - only the score is computed, and the locations of the match are not returned (this makes the algorithm run faster for Local and CFE). | |||||||||||||||||||
NoSelf - compute an alignment where matches of a position with itself are disallowed. This is relevant when aligning a sequence with itself with the purpose of discovering repeated motifs. | |||||||||||||||||||
| Examples | > DB := ReadDb('/home/darwin/DB/SwissProt.Z'):;
Peptide file(/home/darwin/DB/SP45.0/SwissProt45.0(169638448), 163235 entries, 59631787 aminoacids) > DynProgScore(AC(P00083),AC(P00091),DM,Local); [177.7799, 14..92, 19..97] > DynProgScore(AC(P00083),AC(P00091),DM,Global); [144.4751, 1..127, 1..139] > DynProgScore(AC(P00083),AC(P00091),DM,{CFE,JustScore});
[174.0188] > DynProgScore('ADEFGHIKSDEFGHLK','ADEFGHIKSDEFGHLK',DM,NoSelf);
[75.0720, 1..16, 1..16] | ||||||||||||||||||
| See also | Align, Alignment, CreateDayMatrices, MAlign | ||||||||||||||||||