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• backtranseq - Back translate a protein sequence (part of the EMBOSS package)
• charge - Create a protein charge plot (part of the EMBOSS package)
• checktrans - Report stop codons and ORF statistics of a protein (part of the EMBOSS package)
• compseq - Count composition of dimer, trimer and other words in a sequence (part of the EMBOSS package)
• emowse - Identify proteins by mass spectrometry (part of the EMBOSS package)
• freak - Create a residue or base frequency table or plot (part of the EMBOSS package)
• iep - Calculate the isoelectric point of a protein (part of the EMBOSS package)
• mwcontam - Show molecular weights that match across a set of files (part of the EMBOSS package)
• mwfilter - Filter noisy molecular weights from mass spectrometry output (part of the EMBOSS package)
• octanol - Display protein hydropathy (part of the EMBOSS package)
• pepinfo - Plot simple amino acid properties in parallel (part of the EMBOSS package)
• pepstats - Create a report of simple protein sequence information (part of the EMBOSS package)
• pepwindow - Display protein hydropathy (part of the EMBOSS package)
• pepwindowall - Display protein hydropathy for a set of sequences (part of the EMBOSS package)
• Phobius - Predict transmembrane topology and signal peptides from the amino acid sequence of a protein
• ProP - Predict arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks
• PSORT - Predict protein sorting signals and localization sites in amino acid sequences
• SAPS (Statistical Analysis of Protein Sequences) - evaluate a wide variety of protein sequence properties using statistical criteria
• SecretomeP - Predict non-classical (not signal peptide triggered) protein secretion
• SignalP - Predict the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms based on neural networks and Hidden Markov Models
• TMHMM - Predict transmembrane helices based on a Hidden Markov Model