UTILS DATABASE CREATION

 

Database installation

Program nameDescription
aaindexextract Extract data from AAINDEX
cutgextract Extract data from CUTG
printsextract Extract data from PRINTS
prosextract Builds the PROSITE motif database for patmatmotifs to search
rebaseextract Extract data from REBASE
tfextract Extract data from TRANSFAC
allversusall Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values
cathparse Reads raw CATH classification files and writes DCF file (domain classification file)
domainer Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file)
domainnr Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS
domainseqs Adds sequence records to a DCF file (domain classification file)
domainsse Adds secondary structure records to a DCF file (domain classification file)
hetparse Converts raw dictionary of heterogen groups to a file in EMBL-like format
pdbparse Parses PDB files and writes CCF files (clean coordinate files) for proteins
pdbplus Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain
pdbtosp Convert raw swissprot:PDB equivalence file to EMBL-like format
scopparse Reads raw SCOP classification files and writes a DCF file (domain classification file)
seqnr Removes redundancy from DHF files (domain hits files) or other files of sequences
sites Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file)
ssematch Searches a DCF file (domain classification file) for secondary structure matches