Values show the tabulated score for an amino acid substitution. The pair of amino acids involved is shown in single & triple-letter names. The type of codon change is shown:
I = 1st position in codon
II = 2nd position
III = 3rd position
I/II = change in 1st AND 2nd position
I,II = change in 1st OR 2nd position
M = change in all positions (multiple change)
0 = no change
Value=1.4 Min no subs
F-Y Phe-Tyr (II) 1
R-W Arg-Trp (I,I/III) 1
Value=1.3
L-M Leu-Met (I,I/III) 1
F-W Phe-Trp (II/III) 2
Value=1.2
F-L Phe-Leu (I,III,I/III) 1 (several ways)
Value=1.1
B-D Asx-Asp (0,I,III,I/III) 0
B-N Asx-Asn (0,I,III,I/III) 0
E-Z Glu-Glx (0,I,III,I/III) 0
Q-Z Gln-Glx (0,I,III,I/III) 0
I-V Ile-Val (I,I/III) 1
W-Y Trp-Tyr (II/III) 2
Value=1.0
C-Y Cys-Tyr (II,II/III) 1
D-E Asp-Glu (III) 1
Value=0.9
D-Z Asp-Glx (III,I/III) 1
Value=0.8
I-L Ile-Leu (I,I/III) 1
K-R Lys-Arg (II,M) 1
L-V Leu-Val (I,I/III) 1
Value=0.7
A-G Ala-Gly (II,II/III) 1
B-E Asx-Glu (III,II/III) 1
C-S Cys-Ser (I,II/III,I/III)1
D-G Asp-Gly (II,II/III) 1
D-N Asp-Asn (I,I/III) 1
D-Q Asp-Gln (I/III) 2
E-Q Glu-Gln (I,I/III) 1
F-I Phe-Ile (I,I/III) 1
H-Q Gln-His (III) 1
Value=0.6
B-G Asx-Gly (I,M) 1
B-Z Asx-Glx (III,I/III) 1
G-S Glu-Ser (I/II,M) 2
I-M Ile-Met (III) 1
M-V Met-Val (I) 1
Conclude: >0.5 single base changes, plus multiple substitutions which conserve function.
Value=0.5
A-P Ala-Pro (I,I/III) 1
B-Q Asx-Gln (I/III) 2
E-G Glu-Gly (II,II/III) 1
E-N Glu-Asn (I/III) 2
F-M Phe-Met (I/III) 2
H-N His-Asn (I,I/III) 1
H-R His-Arg (II,II/III,M) 1
H-Z His-Glx (III,I/III) 1
L-W Leu-Trp (II,M) 1
Value=0.0
A-I Ala-Ile (I/II) 2
A-K Ala-Lys (I/II,M) 2
A-M Ala-Met (I/II) 2
D-R Asp-Arg (M) 3
E-R Glu-Arg (I/II) 2
M-Q Met-Gln (I/II,M) 2
M-T Met-Thr (II) 1
N-P Asn-Pro (I/II,M) 2
S-Z Ser-Glx (I,M) 1
.
.
.
.
.
.
Value=-0.8
A-W Ala-Trp (I/II,M) 2
C-L Cys-Leu (I/II,M) 2
F-Q Phe-Gln (M) 3
P-W Pro-Trp (I/II,M) 2
P-Y Pro-Tyr (I/II,M) 2
V-W Val-Trp (M) 3
Z-W Glx-Trp (I/II,M) 2
Value=-1.0
D-F Asp-Phe (I/II) 2
G-W Gly-Trp (I) 1
Value=-1.1
D-W Asp-Trp (M) 3
E-W Glu-Trp (I/II) 2
Value=-1.2
C-W Cys-Trp (III) 1
( Bold indicates the program runs as a batch job. most have a corresponding interactive version. Use wisely!!)
( * asterisk indicates that an alternative version beginning with E eg: EAssemble is available as a supplementary program)
Assemble * : joins sequences together
BackTranslate : translates a peptide into a nucleotide sequence
BestFit : displays region of best alignment between two seqs
Chopup : breaks up a file with long records
Circles : a circular plot of RNA secondary structure from FOLD
CodonF * : tabulates codon frequencies
CodonP : plots codon similarity and frequency
CompTable * : creates a symbol comparison table
Compare : compares 2 sequences using word length
Composition : composition and di- and trinucleotide freqs
Compresstext : removes blank lines, spaces etc from files
Consensus * : creates a consensus table from pre-aligned seqs
Correspond * : finds similar patterns of codon choice
Corrupt : random mutation of nucleotide sequence
Count : counts characters,words and lines in file(s)
Crypt * : writes an encrypted (unreadable) file
Dataset : creates a database from any set of GCG sequences
Detab : replaces tabs in file with spaces
Distances : tabulates pair-wise distances within aligned sequences
Diverge * : measures the diff. between 2 nucleotides seqs
DollarToUnder: replaces dollar ($) characters with underscores (_)
Domain : probability of a region of specified composition
Domes : draws a linear plot of folded RNA molecule, after FOLD
DotPlot : makes a 'dot plot' with file from COMPARE, STEMLOOP
EasyGCG : provides a menu for GCG programs
Echo : shows decimal value of each key press (ctrl-Y quits)
Enzymes : types info on available enzymes
Examine : counts the number of characters in each line of a file
ExtractPeptide *: creates a peptide sequence from MAP output
FastA : database search for similarity to a query sequence
Fetch : copies GCG data files to your directory
Figure : makes figures & posters of text & graphics
FindPatterns : searches through sequence(s) for short patterns
FingerPrint * : identifies labelled products of RNA fingerprint
FitConsensus : searches for the best examples of a consensus
Fold : optimal secondary structure for RNA molecule
Fonts : draws tables of all the software-generated fonts
Frames : plots the open reading frames in DNA sequences
FromEMBL : EMBL to GCG format
FromGenbank : GenBank to GCG format
FromIG : Intelligenetics to GCG format
FromPIR : PIR (NBRF) to GCG format
FromStaden * : Staden/Sanger to GCG format
Gap : optimal alignment of 2 sequences using gaps
GapShow : displays 2 sequences marking similarities
GelAssemble : mutiple sequence editor for assembling contigs
GelDisassemble: breaks up the contigs in a fragment assembly project
GelEnter : adds fragments to a fragment assembly project (FAP)
GelOverlap : compares fragments and identifies overlaps in a FAP
GelStart : locks the gelassembly programs onto a particular FAP
GelMerge : automatically aligns the sequences in a FAP
GelView : summarises the structure of the contigs in a FAP
GenHelp : help information on each program in the GCG package
Genmanual : help information arranged by topic
GetSeq * : used by microcomputers to transfer sequences
GetText : similar to GetSeq
GHelp : same as GenHelp but no page waits
GKSterm : selects device for UNIGKS graphics output
HelicalWheel : plots peptide sequence as a helical wheel
Isoelectric : plots the charge of a peptide as a function of pH
KenTau : correlation using Kendall's Tau
Lineup : screen editor for aligning related sequences
ListFile : prints a file on printer attached to terminal
Map : shows restriction sites and possible translations
MapPlot : displays restriction maps graphically
MapSort : tabulates maps by fragment position and size
MFold : optimal and suboptimal RNA secondary structure
Moment : plots helical hydrophobic moment of a protein seq
Motifs : Sequence motif search using PROSITE
Mountains : plots an RNA secondary structure from FOLD ouput
Names : displays filenames in GCG data directories
NewGelStart : Initialises the new FAS to work.
OneCase : changes case of all characters in a file
OverPrint : prints each line of a file as often as specified
Overlap : compares set of DNA sequences to another set
PepData : peptide sequences from GenBank sequence files
PepPlot : plots measures of protein secondary structure
PeptideMap : creates a peptide map of a protein sequence
PeptideSort : tabulates data on peptides
PeptideStruct : secondary structure predictions for peptide sequences
PileUp : Multiple sequence alignments
IPileup : Interactive version of Pileup
PlasmidMap : draws circular plots of plasmid constructs
PlotFold : Graphically displays the output of MFold
PlotSimilarity : average similarity of sequences in a multiple alignment
PlotStructure : plots the output file from PeptideStructure
PlotTest : tests graphic functions used by package
Poster : plots text to help you to label plots/posters
Pretty : displays multiple sequence alignments
Profilemake : calculates a table (protein profile) of aligned sequences
ProfileGap : makes optimal alignment between a protein profile and protein sequence
ProfileScan : compares a sequence to known peptide seq motifs
ProfileSegments: makes optimal alignments from ProfileSearch output
ProfileSearch : uses a protein profile as probe to search protein databases
Publish * : arranges sequences for publication
Red : text formatter to print .RED files
Reformat : converts sequences and tables to GCG format
Repeat * : finds repeats in sequences
Replace : makes character string replacements in text files
Reverse * : reverses and/or complements a sequence
Sample : extracts random fragments from a sequence
Segments : finds where one sequence is similar to others
SeqDif : tabulates sequences differences by position
SeqEd : a screen-oriented sequence editor
Seqformat : makes GCG programs accept data in Staden or GCG format
Setkeys : redefines keys for SEQED, LINEUP, GELENTER, GELASSEMBLE
Shift : moves file to left or right given no. of columns
ShowFiles : creates a documented file of file names
Shuffle : randomizes a sequence
Simplify : simplification scheme for peptide comparisons
Spew : spews characters to a terminal micro-computer
Squiggles : plots RNA secondary structure from FOLD output
StatPlot * : plots columns of numbers in parallel
StemLoop : finds inverted repeats in nucleic acid seqs
Stringsearch : searches files for strings of characters
IStringsearch : interactive version of Stringsearch
TFastA : nucleic-acid database search for similarity to query peptide
Terminator * : searches for prokaryotic terminators
TestCode : identifies protein coding regions in DNA
ToFasta : GCG to FASTA/BLAST format
ToFitch : GCG to Fitch format
ToIG : GCG to Intelligenetics format
ToPIR : GCG to PIR (NBRF) format
ToStaden * : GCG to Staden format
Translate * : translates nucleic acid seqs into peptide seqs
TypeData : displays GCG data files on screen
Ugly : separates sequences in a file produced by PRETTY
Window * : frequencies of di- & tri-residue patterns in a sequence
WordSearch : finds where a sequence is similar to others
Zip : runs BESTFIT, with limits on the permitted gaps
Alltrans : translates a set of aligned nucleotides into protein
Antigenic : identifies potential antigenic regions (Kolaskar)
Basepairplot : plots percentage of di-nucleotides
Bfasta : a version of FASTA that uses the BLOSUM62 matrix
Btfasta : a version of TFASTA that uses the BLOSUM62 matrix
Cpgplot : plots freq of CpG di-nucleotides
Eprogram : several alternative versions of the main programs (asterisked in main list). These usually have command line control added to them.
EGenhelp : help information on each supplementary program
EGenmanual : help information arranged by topic
EGHelp : same as EGenhelp but no page waits
Fastacheck : selects sig. protein alignments in (T)FASTA output
FromFPS : extracts sequences from the Euprom database FPS file
GapAlign : Multiple sequence alignment using GAP
GCGToPhylip : reformats LINEUP data into Phylip format
GClustalV : Multiple sequence alignment of GCG seqs using Clustalv
GelAnalyze : reads Gelstatus output and produces statistics
GelFigure : plots a summary of a contig in a FAP
GelPicture : as Gelview, but also shows a 'Pretty' sequence display
GelStatus : summarises contig quality of the 'project'
Helixturnhelix : potential h-t-h matches in protein sequences
JCAlien : Multiple sequence alignment of GCG seqs using Alien.
Manuals : Creates postscript files of sections of the GCG manual
Mapselect : selects enzymes and writes them to a new enzyme.dat file
Melt : calculates the Tm and percent G+C of a nucleotide seq
Meltplot : plots the melting curve for a nucletotide sequence
Newfeatures : edits the feature table
Palindrome : identifies perfect inverted repeats in nuc seq
Pepallwindow : Pepwindow for multiple sequnence alignments
Pepcoil : identifies coiled-coil regions (Lupas, van Dyke & Stock)
Pepnet : plots 2D helical representations of protein
Pepstats : statistical summary of a protein sequence
Pepwheel : plots periodoc distribution of amino acids
Pepwindow : plots Kyte-Doolittle protein hydropathy
Plotalign : plots amino acid parameters in a multiple alignment
Prdsm : retrieves DNA sequence segments from the EPD file
PrettyBox : Postscript box-shading of multiple sequence alignments
PrettyPlot : boxed (graphical) display of multiple alignments
Sigcleave : potential protein signal cleavage sites
Statsearch : statistics on Wordsearch database searches
ToPrimer : formats a sequence for use with the non-GCG program PRIMER
Tprofilegap : makes optimal alignment between a protein profile and nucleotide sequence
Tprofilesearch : uses a protein profile as probe to search nucleotide databases
Tprofilesegments: makes optimal alignments from TProfileSearch output
Tsegments : As segments - but compares protein to nucleotide
Twordsearch : As wordsearch - but compares protein to nucleotide