Complex informational spectrum analysis for protein sequences (CISAPS) and its web-based server are developed and presented.\nAs recent studies show, only the use of the absolute spectrumin the analysis of protein sequences using the informational spectrum\nanalysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including\nabsolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case\nstudy in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes\ncan present similarities or differences according to the features extracted from CISAPS web server. These associations are probable\nto be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as\nzero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino\nacid indices where each one represents a different property to performthe analysis. This web-based server enables researchers with\nlittle knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.
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