Sequence manipulation (WALIGN)
Introduction.
Big file administration
Creating a big file (BIGFIL)
Initializing a BIGFILE (WALINI)
Checking the big file for double ocurrences (DOUBLS)
Searching for highly homologous pairs (DMATCH)
Recovering original sequences (ORGBCK)
Show contents of BIGFILE (BIGSTS)
Show contents of BIGFILE (MFILES)
Arbitrary sequence numbers
Obtaining the arbitrary sequence numbers (GETARB)
The scoring matrix
Displaying the exchange matrix (SHODAY)
(Re-)setting the exchange matrix (SETMAT)
Input, output and administration of sequences SEQADM
Reading sequences (GETSEQ)
Summary of available sequences (DIRSEQ)
Listing a sequence (LSTSEQ)
Displaying a multi sequence alignment (LSTSQS)
Deleting a sequence (DELSEQ)
Writing a sequence to file (MAKSEQ)
Write internal format multiple sequence file (MAKINT)
Read sequences from a multiple sequence file (GETINT)
Concatenating sequences (CCNSEQ)
Profile administration commands PROF2D
Profile alignment (ALIPRF)
Creating a new profile from aligned sequences (NEWPRF)
Modification of profile with matrix (CNVPRF)
Creating a profile from the soup (SOUPRF)
Aligning two profiles (AL2PRF)
Determine fit of sequence to profile (PCTPRF)
Reading a profile (GETPRF)
Listing profiles (DIRPRF)
Show consensus sequence of profile (LSTPRF)
List the whole profile (SHOPRF)
Deleting a profile from BIGFILE (DELPRF)
Deleting multiple profiles from BIGFILE (DELPRS)
Adding insertions to a profile (INSPRF)
Writing a profile to file (MAKPRF)
Updating a profile from multiple sequence alignment (UPDPRF)
Updating a profile from multiple sequence alignment (UPAPRF)
Make a profile of one sequence (SEQPRF)
Make a GCG-style MSF file (MAKMSF)
Sequence or position weights (PRFSWT)
Correlation analysis WALCOR
Correlation theory
Correlation code administration
Sorting according to class identifiers (GETCMC)
Getting new titles (GETTIT)
Creating a CMC-file (MAKCMC)
Sorting a CMC file (SRTCMC)
skipping residues in correlation analysis
Correlation file (CMCfile) format
create a skip file (MAKTFF)
create a skip file (MAKPTF)
Detection of residues with correlated mutational behaviour
Detection of correlated mutations (CORMUT)
Detection of correlated mutations (CORMUN)
Detection of correlated mutations (CORMUM)
Detection of correlated mutations (CORMUF)
Correlating sequences against external factors
Directed detection of correlations (CORAN1)
Detecting correlations of residues with the class (CORAN2)
Detecting correlations of residues with +/- classes (CORPM1)
Detecting correlations of residues with +/- classes (CORPM2)
Detecting correlations based on residuetypes (CORGR1)
Sorting and selecting sequences WALSRT
Keeping only files with a certain keyword in it (KPNAME)
Deleting files with a certain keyword in it (DELNAM)
Deleting double occurring sequences (KILDBL)
Delete sequences that differ too much (DELALI)
Determining the class of sequences (UNKTYP)
Sorting sequences (SRTPCT)
Sorting sequences (SRTPID)
Sort by accession code (SRTACC)
Sort by accession code (SRTFLN)
Sort by accession code (SRTGMB)
Graphical commands WALGRA
Display sequences (coloured) at the graphics (GRASQS)
Changing the residue colours (COLSQS)
Interactive sequence graphics (SHOW)
Plotting the sequence in the membrane (2DPLOT)
Plotting the sequence in the membrane (PLOT2D)
Boxed sequence alignment output (PRETYG)
Boxed sequence alignment output (PRETYP)
Making a WWW-based database WALSER
Initialize the big server file (GPCINI)
Open the existing big server file (GPCOPE)
Show all statistics about the big server file (GPCSTS)
Shows summary statistics about the big server file (GPCSRC)
Read the classes from _7TM.CLASSES (GPCGCL)
Get the profile information from _7TMPROF.LIST (GPCGPR)
Read the profiles obtained with GPCGPR (GPCRPR)
Use the profiles to classify the sequences (GPCSPL)
Use the profiles to classify the sequences (GPCSEL)
Loop over all classes and update them (GPCMAL)
Read the 7TM directories file (GPCO7T)
Gets the files from 7tmrlist.txt local (GPCG7T)
Other commands
Aligning two sequences (2ALIGN)
Writing aligned sequences in a HSSP file (MAKHSP)
List pairwise identities (SHOIDM)
List pairwise identities (HISTID)
Searching original sequence files (KWCHEK)
Fetching files from databases with GCG (MFETCH)
Hidden commands
Graphical display of pairwise similarities (WLHPID)
Read sequences from LFK style file (WLHLFK)
Over-rule profile gap penalties with (WLHGAP)
Reads sequences from LFK-daily-update-files (WLHLFD)
Checks if sequences have the GPCR fingerprint (WLHFIN)
Delete sequences that mis GPCR fingerprint (WLHDFN)
Do 7TM HSSP process for one molecule class (WLH1ST)
Read sequences from combined swissprot files (WLHSWS)
Delete DNA sequences from the BIGFILE (WLHDNA)
Read sequences from 'list2seq' file (WLHL2S)
Delete fragments from the BIGFILE (WLHDFR)
Cluster sequences after alignment (WLHCLU)
List WALIGN related common parameters and values (WLHSPA)
Creates the file PDB.LIS (WLHCPL)
Searches for decamers that can be good PCR probes (WLHPCR)
Write unaligned sequences as single records in a file (WLHWIN)
As HIDE08, but including gap penaltie updates (WLH2ST)
Reads sequences back that were written with WLHWIN (WLHRIN)
Searches for a fragment of requested weight (WLHGWT)
Writes aligned sequences as single records in a file (WLHWIA)
An option that does something (WLHXXX)
Runs all sequences against all profiles (WLHSPR)
Converts DNA sequence into protein sequence (WLHNAP)
Draws phylogenetic tree (PHYTRE)
Embed sequence space in 3 dimensions (EMBED3)
Parameters for the WALIGN related menus
(SEQSCO)
(PRFSCO)
Pairwise alignment gap open penalty (GAPOPE)
Pairwise alignment gap elongation penalty (GAPELO)
Profile alignment gap open penalty (PRFOPE)
Profile alignment gap elongation penalty (PRFELO)
Character size in PRETY* options (CHRSIZ)
Identities needed for boxing (LIMBOX)
Residues per line in PRETYP options (RESLIN)