A Data set of siRNA sequence:
CUAAUAUGUUAAUUGAUUU
AAUAUGUUAAUUGAUUUAU
GAUUUAUACAAUUCCUUUC
CAAUUCCUUUCAAUUUUAU
CAGACCAAAAUUAAAUAAG
AGACCAAAAUUAAAUAAGA
ACCAAAAUUAAAUAAGAAA
CAAAAUUAAAUAAGAAAGU
UAAGAAAGUUACAUAAGAU
AAGUUACAUAAGAUUCCAU
ACAUAAGAUUCCAUUUGAG
AAGAUUCCAUUUGAGCAUA
CCAUUUGAGCAUACAUAAG
CAUUUGAGCAUACAUAAGG
AUAAGGCCAUGAUACUUUA
GCCAUGAUACUUUAAUGUG
UUAAUGUGAACCACCAUUU
UGUGAACCACCAUUUCUUG
GAACCACCAUUUCUUGGAA
AUUUCUUGGAAGAAAGAAG
UGGAAGAAAGAAGACAUCC
GGAAGAAAGAAGACAUCCA
GAAAGAAGACAUCCAAAUG
AAGACAUCCAAAUGUCCGA
CAUCCAAAUGUCCGAUUCA
UUCCUGGCCAGUCAUCCAG
CCUGGCCAGUCAUCCAGUA
AGUCAUCCAGUAGACUCUC
AGACUCUCUCCACUCUUCA
How can it be converted to a vector of 4, 16, 64, 256, etc. multidimensions using frequencies of its mono, di, tri, tetra nucleotide sub sequences respectively?
This can be answered in many ways depending on what you are really interested in. The problem can be likened to an n-gram problem, where n is 1, 2, 3, 4, ... (your vector of 4, 16, 64, 356, ...) . Essentially one has to break the string into tokens and then sets of tokens of varying length, starting at 1. What is not clear is you want global or per line information also. This can be implemented in any computer language of your choice; take a look at this generic python example http://times.jayliew.com/2010/05/20/a-simple-n-gram-calculator-pyngram/#.VJsBDV4AA.
Thank you Sir for the reply. I am interested in per line information.
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