For proteomics search validation, creation of entrapment databases gives validation of q-value estimates for FDR filtering. There are two levels to entrapment analysis 1) peptide-centric and 2) ...

Specify how many amino acids from the start of a sequence should be left untouched when creating a decoy entry. Specify how many amino acids from the end of a sequence should be left untouched when ...

Check FASTA databases for redundant id lines and protein/nucleotide sequences. If you find that there are redundancies and choose to receive output files which will help you in removing redundancies ...

We pass the blastdb as a fasta file to the pipeline, assuming that the corresponding blast database file are located right next to the fasta file. This is not true for pre-built databases from NCBI ...