Pattern Recognition

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Version 8.1-UNIX

Printed: April 22, 1996 15:51

These programs help you recognize peptide coding regions, terminators, repeats, and other consensus patterns. Several of the programs are for the analysis of sequence composition.


Palindrome searches for perfect inverted repeats in a nucleic acid sequence.


EWindow is a version of Window with command line control. Window makes a table of the frequencies of different sequence patterns within a window as it is moved along a sequence. A pattern is any short sequence like GC or R or ATG. You can plot the output with the program StatPlot.

EStatPlot (+)

EStatPlot is a version of StatPlot with command line control. StatPlot plots a set of parallel curves from a table of numbers like the table written by the Window program. The statistics in each column of the table are associated with a position in the analyzed sequence.


ECodonFrequency tabulates codon usage from sequences and/or existing codon usage tables. The output file is correctly formatted for input to the CodFish, CodonPreference, Correspond, and Frames programs.

ECodonFrequency is a modified version of GCG version 7's CodonFrequency with command line control added.


EConsensus calculates a consensus sequence for a set of pre-aligned short nucleic acid sequences by tabulating the percent of G, A, T, and C for each position in the set. GCG's FitConsensus uses the EConsensus output table as a probe to search for the best examples of the derived consensus in other nucleotide sequences.


ECorrespond looks for similar patterns of codon usage by comparing codon frequency tables.


ERepeat finds direct repeats in sequences. You must set the size, stringency, and range within which the repeat must occur; all the repeats of that size or greater are displayed as short alignments. ERepeat is a version of GCG's old Repeat with command line control.


ETerminator searches for prokaryotic factor-independent RNA polymerase terminators according to the method of Brendel and Trifonov. ETerminator is a version of GCG's old Terminator with command line control.