scoring, cyclic permutation

# scoring, cyclic permutation ## Syntax This parameter can have the values yes or no. ## Notes This parameter was introduced in version 2006.04.01 The default value for this parameter is no. ## Description X! Tandem performs a detailed statistical analysis on the peptides found during a search to determine which results are statistically valid. This analysis depends on comparing the best result of a search to the distribution of all other peptide sequences that matched the parent ion mass tolerance test. While it only takes approximately 300 peptides to generate a reliable distribution, if a very small sequence collection is used, there may be too few matching peptides to generate a reliable distribution. If the distribution is too small, default values are used to calculate the expectation value for a result. While the default values are reasonable, they may lead to over or under estimation of the true expectation value. To try to generate a distribution for very small sequence collections, setting this parameter to yes generates a set of cyclic permutations of each peptide that falls within the parent ion tolerance. This set of peptides, given the sequence "YGGFLR" would be: YGGFLR - the initial sequence RYGGFL LRYGGF FLRYGG GFLRYG GGFLRY RLFGGY YRLFGG GYRLFG GGYRLF FGGYRL LFGGYR Each of these alternative sequences is scored and used to construct the scoring distribution, but they are not stored in the output, even if they have better scores than the initial peptide sequence. see also: scoring, include reverse X! TANDEM API description project