HmmerPfam
Compares
one or more sequences to a database of profile hidden Markov models,
such as the Pfam library,
in
order to identify known domains within the sequences.
PeptideStructure
Makes
secondary structure predictions for a peptide sequence.
These
predictions include (in addition to alpha, beta, coil, and turn) measures
for antigenicity, flexibility, hydrophobicity, and surface
probability. The predictions are displayed graphically.
CoilScan
Locate
coiled-coil segments in protein sequences. .
HTHScan
Locate
helix-turn-helix motifs in protein sequences.
SPScan
Locate
secretory signal peptides in protein sequences.
PeptideSort
Shows
the peptide fragments from a digest of an amino acid sequence.
It
sorts the peptides by weight, position, and HPLC relative
retention, and shows the composition of each peptide. It also
prints a summary of the composition of the whole protein.
PepPlot
Plots
predicted protein secondary structure and hydropathy plot. .
Moment
Makes
a contour plot of the helical hydrophobic moment of a peptide
sequence.
HelicalWheel
Plots a peptide sequence as a helical wheel to help you recognize
amphiphilic regions or beta sheets.
Isoelectric
Plots the charge as a function of pH for a peptide sequence.
TransMem
Scans
for likely transmembrane helices in a peptide sequence.
OTHERS
Motifs
Looks for sequence motifs by searching through proteins for the
patterns defined in the PROSITE Dictionary of Protein Sites
and Patterns. Motifs can display an abstract of the
current literature on each of the motifs it finds.