diff --git a/localcider/sequenceParameters.py b/localcider/sequenceParameters.py index feef29e..dd902a9 100644 --- a/localcider/sequenceParameters.py +++ b/localcider/sequenceParameters.py @@ -577,11 +577,10 @@ def get_linearComplexity(self, complexityType="WF", alphabetSize=20, userAlphabe WF - Wooton-Federhen complexity [1] - LC - Linqguistic complexity [ ] + LC - Linguistic complexity [2] - LZW - Lempel-Ziv-Welch [ ] + LZW - Lempel-Ziv-Welch [3] - RHP - Richardson, Holehouse, Pappu (Default = 'WF') @@ -599,9 +598,9 @@ def get_linearComplexity(self, complexityType="WF", alphabetSize=20, userAlphabe windowSize | Sliding window size over which complexity is calculated (default=10) stepSize | Size of steps taken as we define a new sliding window. Default is - 1 and should probably always be used... + 1 (recommended to keep at 1) - wordSize | Relevant for linguistic complexity (need more details!) + wordSize | Relevant for linguistic complexity OUTPUT: -------------------------------------------------------------------------------- @@ -611,7 +610,7 @@ def get_linearComplexity(self, complexityType="WF", alphabetSize=20, userAlphabe Predefined alphabets shown below - all except eleven are based on alphabets defined in - the reference below. + the reference below [4] two - [(LVIMCAGSTPFYW), (EDNQKRH)] three - [(LVIMCAGSTP), (FYW), (EDNQKRH)] @@ -626,10 +625,20 @@ def get_linearComplexity(self, complexityType="WF", alphabetSize=20, userAlphabe eighteen - [(LM), (VI), (C), (A), (G), (S), (T), (P), (F), (Y), (W), (E), (D), (N), (Q), (K), (R), (H)] twenty - all twenty! + -------------------------------------------------------------------------------- + REFERENCES + [1] Wootton, J. C., & Federhen, S. (1993). Statistics of local complexity in amino acid sequences and sequence databases. Computers & Chemistry, 17(2), 149-163. + + [2] Troyanskaya, O. G., Arbell, O., Koren, Y., Landau, G. M., & Bolshoy, A. (2002). Sequence + complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic + complexity. Bioinformatics , 18(5), 679–688. + + [3] Lempel, A.& Ziv, J. (1976). On the complexity of finite sequence. IEEE Trans. Inf. Theory, + vol. IT-22, no. 1, 75-81. - [n]: Murphy, L. R., Wallqvist, A., & Levy, R. M. (2000). Simplified amino acid alphabets for + [4] Murphy, L. R., Wallqvist, A., & Levy, R. M. (2000). Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Engineering, 13(3), 149-152.