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.