Protein sequence analysis

• Pattern searching
• Protein structure analysis
• Protein properties
• Enzyme kinetics
• Protein display

• Pattern searching

PRATT

• pratt: Patterns discovery in sets of unaligned protein sequences.




PROSE

• prose: Search Prosite patterns in a sequence.




SIG

• sig: Multiple Prosite motifs searching.




SCAN_FOR_MATCHES

• scan_for_matches: Scan nucleotide or protein sequences for matching patterns.




CONSENSUS

• consensus: Identification of consensus patterns in unaligned sequences.




EMBOSS

• antigenic: Finds antigenic sites in proteins.
• digest: Protein proteolytic enzyme or reagent cleavage digest.
• epestfind: Finds PEST motifs as potential proteolytic cleavage sites.
• fuzzpro: Protein pattern search.
• fuzztran: Protein pattern search after translation.
• helixturnhelix: Report nucleic acid binding motifs.
• oddcomp: Find protein sequence regions with a biased composition
• patmatdb: Search a protein sequence database with a motif.
• patmatmotifs: Search a motif database with a protein sequence.
• preg: Regular expression search of a protein sequence.
• pscan: Scans proteins using PRINTS database.
• sigcleave: Reports protein signal cleavage sites.

• Protein structure analysis

DSSP [local access only]

• dssp: Discrimination of protein secondary structure class.




PREDATOR

• predator: Protein secondary structure prediction from sequences.




TOPPRED

• toppred: Topology prediction of membrane proteins.




EMBOSS

• garnier: Predicts protein secondary structure
• helixturnhelix: Report nucleic acid binding motifs.
• hmoment: Hydrophobic moment calculation
• pepcoil: Predicts coiled coil regions.
• pepnet: Shows protein sequences as helices.
• pepwheel: Displays proteins as a helical net.
• tmap: Displays membrane spanning regions.

• Protein properties

SAPS

• saps: Statistical Analysis of Protein Sequences.




PSORT

• psort: Predicts protein subcellular localization sites from their amino acid sequences.




EMBOSS

• backtranambig: Back translate a protein sequence to ambiguous codons.
• backtranseq: Back translate a protein sequence.
• charge: Protein charge plot.
• compseq: Count composition of dimer/trimer/etc words in a sequence
• checktrans: ORF property statistics.
• emowse: Protein identification by mass spectrometry.
• freak: Base frequency table or plot
• hmoment: Hydrophobic moment calculation.
• iep: Calculates the isoelectric point of a protein.
• mwfilter: Filter noisy molwts from mass spec output.
• octanol: Plots difference in solubility in octanol and water for a window of residues.
• pepinfo: Plots simple amino acid properties in parallel
• pepstats: Protein statistics.
• pepwindow: Displays protein hydropathy.
• pepwindowall: Displays protein hydropathy of a set of aligned sequences.
• prettyplot: Replacement for EGCG's prettyplot. Also to provide text output from sequence alignments.

• Enzyme kinetics

EMBOSS

• findkm: Calculates Km and Vmax for an enzyme reaction.

EMBOSS

• pepnet: Displays proteins as a helical net
• pepwheel: Shows protein sequences as helices