Protein Analysis

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Version 8.1-UNIX

Printed: April 22, 1996 15:51

Most GCG programs work on either protein or nucleotide sequences. The programs in this chpater, however, do analyses specific to protein sequences. The first two programs identify sequence motifs in protein sequences. The next three programs make predictions about peptide isolation. The last five look at secondary structure, hydrophobicity, and antigenicity.

PepCoil (+)

PepCoil identifies potential coiled-coil regions of protein sequences using the algorithm of Lupas A, van Dyke M & Stock J (1991).

PepNet (+)

PepNet is a program to view the two-dimensional helical representation of protein sequences.

PepWheel (+)

PepWheel is a program to view the periodic distribution of amino acid residues in protein sequences.

PepWindow (+)

PepWindow plots measures of protein hydrophobicity according to the method of Kyte and Doolittle.


PepStats gives a short statistical summary on the composition of a protein sequence and gives the molecular weight and isoelectric point.


SigCleave uses the von Heijne method to locate signal sequences, and to identify the cleavage site. The method is 95% accurate in resolving signal sequences from non-signal sequences with a cutoff score of 3.5, and 75-80% accurate in identifying the cleavage site. The program reports all hits above a minimum value.


Antigenic looks for potential antigenic regions using the method of Kolaskar.


HelixTurnHelix uses the method of Dodd and Egan to determine the significance of possible helix-turn-helix matches in protein sequences.


DoDayhoffStat compares the composition of a protein sequence against the Dayhoff statistic for protein composition. The closer the Dayhoff Stat value is to 1.0 the better the composition of the protein sequence fits with the theoretical value.


PepCount reports the number of occurrences of residues at a given position in protein sequences.


EPeptideSort shows the peptide fragments from a digest of an amino acid sequence. It sorts the peptides by weight, position, and HPLC retention at pH 2.1, and shows the composition of each peptide. It also prints a summary of the composition of the whole protein. EPeptideSort is a modified version of GCG's PeptideSort which has additional options to control output of peptides sorted by weight, retention and position.