command of alignment for general sequences

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huda nawaf
huda nawaf el 27 de Nov. de 2011
hi, is there a command of sequence alignment for any sequence generally ? I did not mean swalign or nwalign, these just for biological sequences. if not are there anyone wrote a code of sequence alignment for non biological sequences in matlab?
thanks
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huda nawaf
huda nawaf el 28 de Nov. de 2011
thanks walter, i will see the link
sven , I mean any sequence of integers or characters.
There is algorithms of seq. alignment but designed for DNA or protein sequences.
I hope to find for general seq.
thanks
huda nawaf
huda nawaf el 29 de Nov. de 2011
thanks walter,
i did not see the last comment by Lucio.
really thanks

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Hin Kwan Wong
Hin Kwan Wong el 28 de Nov. de 2011
What sequence? If you mean any two numerical sequences which are correlated. Their alignment can be done by using cross correlation and finding where the peak is in terms of the delay, then shifting one of the sequence by the delay.
xcorr = ifft(fft(signalA).*conj(fft(signalB));
delay = find((xcorr==max(xcorr))==1);
AlignedA = circshift(signalA,1-delay);

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