-
- seqed sequence editor.
- setkeys redefines the keyboard for seqed, lineup &
elineup
(See Multiple Sequence Analysis for (e)lineup).
- newfeatures useful for editing feature tables within
sequence files.
NB: Do not attempt to edit any GCGformat
sequence files with any normal text editors available on the system. The
other programmes in the GCG package will think your sequence
file has become corrupted. Use one of the GCG or
EGCG sequence editors instead.
Return to Programmes organised by function
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- gelstart to start doing a fragment assembly project.
- newgelstart to start using the new fragment assembly
system.
- gelenter adds fragments to a fragment assembly project.
- geloverlap compares sequences in a fragment assembly
project.
- gelassemble multiple sequence editor for creating contigs.
- gelview displays structure of existing contigs.
- geldisassemble breaks up the contigs into single fragments
again.
- gelmerge automatically aligns the seqeunces in a fragment
assembly project into contigs.
- gelstatus produces a summary report of the quality of
each contig in a fragment assembly database.
- gelpicture displays displays a diagram of the gel
alignments and a printout of the aligned gel sequences and consensus.
- gelfigure produces a graphical report of the status of
a contig.
- gelanalyze produces project statistics by the method of
Lander and Waterman.
Return to Programmes organised by function
-
- map displays both strands of DNA with restriction map and
protein translations.
- mapplot shows all possible restriction sites in a sequence
graphically.
- mapsort finds and sorts restriction enzyme cuts in DNA
sequence.
- mapselect selects restriction enzymes by name or by their
ability to cut a given sequence.
- fingerprint identifies the products of T1 ribonuclease
digestion.
- efingerprint version of GCG's old FingerPrint with
command line control.
- prime selects oligonucleotide primers for a template DNA
sequence.
Return to Programmes organised by function
-
- compare compares two protein or nucleic acid sequences.
- dotplot makes a dotplot with output file of 'compare',
'fold' or 'stemloop'.
- bestfit makes optimal alignment of two distantly related
sequences.
- gap makes optimal alignment of two closely related
sequences.
- gapshow displays the alignment of two sequences.
- diverge measures % divergence of proteins by method of
Perler & Efstratiadis.
- ediverge measures the percent divergence of two protein
coding sequences.
- overlap compares two sets of DNA sequences to each other
in both orientations.
- eoverlap compares two sets of DNA sequences.
- bigeoverlap eoverlap with a very high limit on total
sequence length.
- filteroverlap filters only overlaps with specified value
for alignments from eoverlap.
- nooverlap identifies the places where a group of
nucleotide sequences do not share any common subsequences.
- framealign creates an optimal alignment between a protein
sequence and the codons in all possible reading frames of a NA sequence.
Return to Programmes organised by function
-
- fasta sensitive database search.
- tfasta sensitive database search between peptide file and
DNA database.
- fastacheck FastaCheck selects significant alignments
from a (T)Fasta output file.
- blast database search for similar sequences (see toblast).
- wordsearch search by method of Wilbur & Lipman, 'segments'
uses output.
- twordsearch TWordSearch identifies DNA sequences similar
to a protein query.
- stssearch StsSearch looks for primer pairs in a set of
sequences.
- segments aligns and displays segments of similarity found
by 'wordsearch'.
- tsegments TSegments aligns and displays the segments
of similarity found by TWordSearch.
- findpatterns looks for patterns in sequences, allows for
ambiguity and mismatches
- rfindpatterns FindPatterns with fixed reporting of 5'
flanking residues.
- patternplot graphical representation of
FindPatterns.
- stringsearch finds sequences by searching their comments
for words e.g., "Human".
- lookup does a similar keywording job to stringsearch, but
faster!
- names finds GCG data files and sequences by name.
- fetch gets sequences from the databases & GCG data files.
- newfetch copies GCG sequences or fragments or data files
from the GCG database.
- dataset creates a GCG database from any set of GCG format sequences.
- framesearch searches a group of protein sequences for
similarity to one or more nucleotide query sequences, or searches a group of
nucleotide sequences for similarity to one or more protein query sequences.
Return to Programmes organised by function
-
- pileup creates a multiple sequence alignment from related
sequences.
- profalign aligns two alignments ( or sequences )
together.
- multalign simultaneous alignment for two or more DNA or
protein sequences.
- eclustalw calculates a multiple alignment of nucleic acid
or protein sequences.
- clustree computes a phylogenetic tree (from Clustalw).
- sortconsensus identifies the strong consensus regions
of an alignment and reports them in sorted order.
- lineup multiple sequence editor.
- elineup is a screen editor for editing multiple sequence
alignments.
- pretty displays multiple sequence alignmernts & consensus
sequence.
- prettyplot displays multiple sequence alignments and
calculates a consensus sequence.
- prettybox displays multiple sequence alignments and
calculates a consensus sequence.
- plotsimilarity plots running average of multiple alignment
similarity.
- eplotsimilarity plots the running average of the
similarity among the sequences in a multiple sequence alignment.
- profilemake calculates a profile of a group of sequences
for 'profilesearch'.
- profilesearch uses profile created by 'profilemake' to search
database.
- tprofilesearch uses a profile to search the nucleotide
database.
- profilesegments makes optimal alignments using output of
'profilesearch'.
- tprofilesegments makes optimal alignments showing the
segments of similarity found by TProfileSearch.
- profilegap makes optimal alignment between profile and a
sequence.
- tprofilegap makes an optimal alignment between a profile
and a sequence.
- profileplot produces a graphical report of the frequency
of patterns in sequences.
- plotalign plots the mean and range of values for any
amino acid parameter you supply.
- pepallwindow plots measures of protein hydrophobicity
according to the method of Kyte and Doolittle.
- polydot compares two sets of sequences, draws a dotplot
for each pair of sequences, and reports all identical matches of a specified
length.
Return to Programmes organised by function
-
- codonpreference framespecific genefinder.
- testcode plots measure of nonrandomness of composition
at every 3rd base.
- frames shows open reading frames for all 6 translations
of DNA.
- repeat finds repeats in nucleotide sequences.
- erepeat version of GCG's old Repeat with command
line control.
- window makes table of frequency of patterns, plot the
output with 'statplot'.
- ewindow version of Window with command line
control.
- statplot plots set of parallel curves from table made by
'window'.
- estatplot version of StatPlot with command line
control.
- composition determines composition of sequences.
- terminator looks for prokaryote factor independant RNA
polymerase terminators.
- eterminator version of GCG's old Terminator with
command line control.
- consensus creates a consensus sequence from a set of
aligned sequences.
- 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.
- fitconsensus probes a sequence for the best fit to a
'consensus' sequence.
- codonfrequency tabulates codon usage used by
'codonpref', 'correspond', 'frames'.
- ecodonfrequency tabulates codon usage from sequences
and/or existing codon usage tables.
- correspond looks for similar patterns of codon usage
by comparing codon tables.
- ecorrespond looks for similar patterns of codon usage
by comparing codon frequency tables.
- palindrome searches for perfect inverted repeats in
a nucleic acid sequence.
Return to Programmes organised by function
-
- mfold predicts optimal and suboptimal RNA secondary
RNA structure.
- plotfold graphically displays the output of mfold.
- foldrna 2ry RNA structure, used by 'squiggles',
'mountains', 'circles', 'dotplot'.
- squiggles uses output of 'fold' to plot RNA secondary
structure nicely.
- circles uses output of 'fold' to plot RNA secondary
structure.
- domes uses output of 'fold' to plot RNA secondary
structure.
- mountains uses output of 'fold' to plot RNA secondary
structure.
- stemloop finds inverted repeats in a sequence.
Return to Programmes organised by function
-
- isoelectric plots the charge as a function of pH for
any peptide sequence.
- motifs uses the PROSITE database to find patterns
in protein sequences.
- profilescan uses a database of profiles to find
structural motifs in proteins.
- peptidemap creates peptide map of an amino acid
sequence.
- peptidesort shows peptides from a digest of an amino
acid sequence.
- epeptidesort shows the peptide fragments from a digest
of an amino acid sequence.
- pepplot makes parallel plot of protein 2ry structure
and hydrophobicity.
- peptidestructure predicts 2ry structure for a peptide,
used by 'plotstructure'.
- plotstructure plot output of 'peptidestructure'.
- pepcoil identifies potential coiled-coil regions of
protein sequences.
- pepnet views the two-dimensional helical representation
of protein sequences.
- pepwheel view the periodic distribution of amino acid
residues in protein sequences.
- pepwindow plots measures of protein hydrophobicity
(Kyte and Doolittle).
- pepcount reports the number of occurrences of residues
at a given position in protein sequences.
- pepstats summary of the composition, molecular weight
and isoelectric point of a peptide.
- sigcleave uses the von Heijne method to locate signal
sequences, and to identify the cleavage site.
- antigenic looks for potential antigenic regions using
the method of Kolaskar.
- moment makes contour plot of helical hydrophobic moment
of a peptide sequence.
- helicalwheel plots a peptide structure as a helical
wheel.
- helixturnhelix determine the significance of possible
helix-turn-helix matches in protein squences.
- dodayhoffstat compares the composition of a protein
sequence against the Dayhoff statistic for protein composition.
Return to Programmes organised by function
-
- distances makes table of pairwise distances within a
group of aligned sequences.
- homologies makes a table of the pair-wise distances
within a group of aligned sequences.
- growtree creates a phylogenetic tree from a distance
matrix produced by 'distances'.
- tophylip writes GCG sequences into a single file in
Phylip format.
- phylip2tree displays trees computed with one of the
PHYLIP-programs in GCG style.
- NewDiverge estimates the number of substitutions per
site between two nucleic acid sequences that code for proteins.
Return to Programmes organised by function
-
- translate translate nucleotide sequences into peptide
sequences.
- etranslate version of GCG's old Translate program with
command line control added.
- transall simple script which outputs all 6 frames into
separate files.
- pepdata translates coding regions of GenBank DNA into
peptides, also 6 frames.
- alltrans translates a set of aligned nucleotide sequences
into protein.
- mytrans translates part of a nucleotide sequence into
protein.
- backtranslate create nucleotide sequence from an amino
acid sequence.
- extractpeptide writes peptide sequence from output of
'map'.
- eextractpeptide version of ExtractPeptide with command
line control.
Return to Programmes organised by function
-
- assemble conatenates sequences.
- eassemble command line control added to
GCG's assemble.
- reverse reverses and/or complements sequences.
- ereverse command line control added to
GCG's reverse.
- shuffle randomises sequences.
- simplify simplifies peptide sequences into broad amino
acid categories.
- comptable creates symbol comparison tables, e.g., for
simplify.
- ecomptable command line control added to
GCG's comptable.
- corrupt randomly introduces small errors into a
nucleotide sequence.
- pepcorrupt randomly introduces small substitutions,
insertions, and deletions.
- sample extracts sequence fragments randomly from
sequences.
Return to Programmes organised by function
-
- plasmidmap draws circular plot of a plasmid construct.
- figure makes figures and posters. Can incude graphics
from other GCG programmes.
- red text formatter.
- publish arranges sequences for publication.
Return to Programmes organised by function
-
- reformat makes sequence files readable by GCG programmes.
- creformat Reformats sequence file(s), scoring matrix
file(s), or enzyme data file(s).
- fromstaden reformats sequence files from Staden format
to GCG.
- tostaden reformats sequence files from GCG to Staden format.
- efromstaden reformats staden sequence(s) from fasta into
GCG format files.
- etostaden version of GCG's ToStaden with command line control.
- fromig reformats sequence files from Intelligenetics
(SEQ) format to GCG.
- toig reformats sequence files from GCG to Intelligenetics (SEQ) format.
- fromembl reformats sequence from EMBL format to GCG.
- toembl reads an EMBL entry from a GCG sequence database as EMBL file format.
- fromgenbank reformats sequence files from GenBank format
to GCG.
- togenbank reads a GenBank entry from a GCG sequence database as GenBank file format.
- frompir reformats sequence files from PIR format to GCG.
- topir reformats sequence files from GCG to PIR format.
- topirall converts a list of sequences into PIR format.
- fromfasta reformats sequence files from fasta format
to GCG.
- efromfasta reformats fasta sequence(s) from fasta into
GCG format files.
- toblast combines any set of GCG sequences into a database that you can search with blast.
- totext converts a sequence into plain text format.
- toprimer formats a GCG sequence file into a PRIMER compatible file.
- torelate creates an input file for the NBRF RELATE
program.
- egetseq version of GCG's GetSeq with command line control.
Return to Programmes organised by function
-
-
- melt calculates the melting temperature and G+C % of
NA sequences.
- meltplot plots the melting curve for a nucleic acid
sequence.
- basepairplot plots the percentage occurence and the
observed over expected frequency of a di-nucleotide pair relative to their
position in a nucleic acid sequence.
- cpgplot CpGPlot plots the frequency of occurence of
CpG di-nucleotides and C and G percentage relative to their position in a
sequence.
- cpgreport CpGReport looks for potential CpG islands
in a nucleotide sequence.
- chaos makes a CHAOS game representation of a nucleic
acid sequence.
- codfish calculates a set of codon usage statistics
for a sequence using a specified codon usage table.
- wordcount counts the commonest words in a sequence
and reports them in order of frequency and sequence.
- wordup detects statistically significant oligonucleotide
patterns from six to nine nucleotides long in the sequences under investigation.
- poland simulates transition curves of double-stranded DNA.
- genetrans extracts and/or translates coding regions as
defined in the feature table of sequences stored in the EMBL or Genbank
databases.
- gapframe moves all gaps in a DNA sequence reading frame
to be at codon boundaries.
- prima selects oligonucleotide primers for a template DNA
sequence.
- quicktandem scans for potential tandem repeats in a
nucleotide sequence.
- tandem looks for multiple tandem repeats of a given size
in a nucleotide sequence.
- inverted looks for imperfect inverted repeats in a
nucleotide sequence.
- ecomposition determines the composition of
sequence(s).
Return to Programmes organised by function
-
- genhelp display the help files of these programmes.
- egenhelp help organized by program name.
- egenman help organized by function categories.
- 8.1_Whats_New what's new in version 8.1-unix of the
EGCG extensions to the GCG package.
- setplot allows you to change the device that plots
come out on.
- showplot shows what your graphics device is currently
set to.
- plottest plots a test pattern for you to check your
graphics output.
- echokey shows the decimal value of each key you press.
- fonts draws tables showing each of the fonts used.
- wpi & runs the graphical Wisconsin Package Interface.
- wpi -small & runs the small screen version.
Return to Programmes organised by function
