From: SeqHound: biological sequence and structure database as a platform for bioinformatics research
Input File | Resource | Parser | Tables Modified | Module |
---|---|---|---|---|
ASN.1 sequences | ftp://ftp.ncbi.nih.gov/ncbi-asn1/*.asoftp://ftp.ncbi.nih.gov/refseq/cumulative/*.bna | mother | ASNDB, PARTI, NUCPOT, ACCDB, PUBSEQ, TAXGI, SENDB, SENGI | core |
ASN.1 sequences | ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/*.asoftp://ftp.ncbi.nih.gov/refseq/daily/*.bna | update | ASNDB, PARTI, NUCPOT, ACCDB, PUBSEQ, TAXGI, SENDB, SENGI | core |
FASTA nr database | redund | REDUND | redundb | |
List of complete genomes (flat file) | http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/slritools/slri/seqhound/genomes/chromff | chrom | CHROM | gendb |
ASN.1 for complete genomes | comgen | TAXGI, ACCDB | gendb | |
Taxonomy release (flat file) | ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar | importtaxdb | TAX, GCODE, DIV, DEL, MERGE | taxdb |
ASN.1 MMDB release | cbmmdb | MMDB, MMGI | strucdb | |
MMDB (database table) | MMDB table | vastblst | DOMDB | strucdb |
3-D chain BLAST sets (flat file) | pdbrep | DOMDB | strucdb | |
FASTA nr database | nblast | nrB | neigdb | |
BLAST ASN.1 results | nrB table available nrB and nrN tables availables at ftp://ftp.mshri.on.ca/pub/NBLAST | nbraccess | nrN | neigdb |
LL_tmpl (flat file) | llparser | LL_OMIM, LL_GO, LL_LLINK, LL_CDD | lldb | |
gene_associaton.com pugen.GenBank/Swissprot (flat files) | addgoid | LL_GO | lldb | |
function.ontology process.ontology component.ontology (flat files) | goparser | GO_PARENT, GO_NAME, GO_REFERENCE, GO_SYNONYM | godb | |
CDD database | domname | DOMNAME | rpsdb | |
FASTA nr database and CDD database | ftp://ftp.ncbi.nih.gov/blast/db/nr; ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/ DOMNAME and RPSDB tables available at ftp://ftp.mshri.on.ca/pub/RPS | rpsdb | RPSDB | rpsdb |