Repeat & Vector Masking
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[Genetic Information Research Institute] The CENSOR web server allows users to have query sequences aligned against a reference collection of human, rodent, or plant repeats.
[Georgia Tech] This program is used for gene prediction in sequences. “The GeneMark program relies upon an Inhomogeneous Markov Model approach combined with training datasets to predict genes. Along with predicting genes, it can use RBS models to predict RBS sites and predict frameshifts.”
[NCBI] “VecScreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin.” It is designed to help researchers identify and remove any segments of vector origin prior to sequence analysis or submission.