Sequence manipulation (WALIGN)
Introduction.
short list of WALIGN commands
WALIGN related menus (SEQADM)
WALIGN related menus (PROF2D)
WALIGN related menus (CORREL)
WALIGN related menus (WALGRA)
WALIGN related menus (WALSDB)
WALIGN related menus (WALSRT)
Big file administration
Creating a big file (BIGFIL)
Checking the big file for double ocurrences (DOUBLS)
Searching for highly homologous pairs (DMATCH)
Recovering original sequences (ORGBCK)
Sorting sequences (SRTPCT)
The scoring matrix
Displaying the exchange matrix (SHOMAT)
(Re-)setting the exchange matrix (SETMAT)
Input and output 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)
Reading a file from the swissprot database (GETSWS)
Write internal format multiple sequence file (MAKINT)
Read sequences from a multiple sequence file (GETINT)
Profile administration commands (PROF2D)
Profile alignment (ALIPRF)
Creating a new profile from aligned sequences (NEWPRF)
Aligning two profiles (AL2PRF)
Determine fit of sequence to profile (PCTPRF)
Reading a profile (GETPRF)
Show consensus sequence of profile (LSTPRF)
List the whole profile (SHOPRF)
Deleting a profile from bigfile (DELPRF)
Adding insertions to a profile (INSPRF)
Writing a profile to file (MAKPRF)
Updating a profile from multiple sequence alignment (UPDPRF)
Make a profile of one sequence (SEQPRF)
Make a gcg msf file (MAKMSF)
Correlation analysis (CORREL)
Correlation code administration
Sorting according to class identifiers (GETCMC)
Creating a CMC-file (MAKCMC)
Sorting a CMC file (SRTCMC)
skipping residues in correlation analysis
create a skip file (MAKTFF)
create a skip file (MAKPFF)
The correlation file
Detection of residues with correlated mutational behaviour
Detection of correlated mutations (CORMUT)
Detection of correlated mutations (CORMUN)
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)
Graphical commands (WALGRA)
Display sequences (coloured) at the graphics (GRASQS)
Changing the residue colours (COLSEQ)
Interactive sequence graphics (SHOW)
Plotting the sequence in the mambrane (2DPLOT)
Database operations (WALSDB)
Prepare the database for fast access (PREPDB)
Fast screening of the database (FASTB)
Run a profile against the database (DBPROF)
Listing a swissprot file (LSTSWP)
Scan the database with a profile (GENPRF)
Scan the database with keywords (GENTST)
Other commands
Aligning two sequences (2ALIGN)
Writing aligned sequences in a HSSP file (MAKHSP)
List pairwise identities (SHOIDM)
List pairwise identities (PCTID)
Clustering sequences (CLUSEQ)
Searching original sequence files (KWCHEK)
Fetching files from databases with GCG (MFETCH)