EMBOSS

UTILS DATABASE CREATION

Database installation

Program name Description

aaindexextract Extract amino acid property data from AAINDEX

cutgextract Extract codon usage tables from CUTG database

jaspextract Extract data from JASPAR

printsextract Extract data from PRINTS database for use by pscan

prosextract Processes the PROSITE motif database for use by patmatmotifs

rebaseextract Process the REBASE database for use by restriction enzyme applications

tfextract Process TRANSFAC transcription factor database for use by tfscan

cathparse Generates DCF file from raw CATH files

domainnr Removes redundant domains from a DCF file

domainseqs Adds sequence records to a DCF file

domainsse Add secondary structure records to a DCF file

scopparse Generate DCF file from raw SCOP files

ssematch Search a DCF file for secondary structure matches

allversusall Sequence similarity data from all-versus-all comparison

seqnr Removes redundancy from DHF files

domainer Generates domain CCF files from protein CCF files

hetparse Converts heterogen group dictionary to EMBL-like format

pdbparse Parses PDB files and writes protein CCF files

pdbplus Add accessibility and secondary structure to a CCF file

pdbtosp Convert swissprot:PDB codes file to EMBL-like format

sites Generate residue-ligand CON files from CCF files

Program name	Description
aaindexextract	Extract amino acid property data from AAINDEX
cutgextract	Extract codon usage tables from CUTG database
jaspextract	Extract data from JASPAR
printsextract	Extract data from PRINTS database for use by pscan
prosextract	Processes the PROSITE motif database for use by patmatmotifs
rebaseextract	Process the REBASE database for use by restriction enzyme applications
tfextract	Process TRANSFAC transcription factor database for use by tfscan
cathparse	Generates DCF file from raw CATH files
domainnr	Removes redundant domains from a DCF file
domainseqs	Adds sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
scopparse	Generate DCF file from raw SCOP files
ssematch	Search a DCF file for secondary structure matches
allversusall	Sequence similarity data from all-versus-all comparison
seqnr	Removes redundancy from DHF files
domainer	Generates domain CCF files from protein CCF files
hetparse	Converts heterogen group dictionary to EMBL-like format
pdbparse	Parses PDB files and writes protein CCF files
pdbplus	Add accessibility and secondary structure to a CCF file
pdbtosp	Convert swissprot:PDB codes file to EMBL-like format
sites	Generate residue-ligand CON files from CCF files