Table 2

Parsers and resource files needed to build and update SeqHound.

Input File

Resource

Parser

Tables Modified

Module


ASN.1 sequences

ftp://ftp.ncbi.nih.gov/ncbi-asn1/ webcite*.aso ftp://ftp.ncbi.nih.gov/refseq/cumulative/ webcite*.bna

mother

ASNDB, PARTI, NUCPOT, ACCDB, PUBSEQ, TAXGI, SENDB, SENGI

core

ASN.1 sequences

ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/ webcite*.aso ftp://ftp.ncbi.nih.gov/refseq/daily/ webcite*.bna

update

ASNDB, PARTI, NUCPOT, ACCDB, PUBSEQ, TAXGI, SENDB, SENGI

core

FASTA nr database

ftp://ftp.ncbi.nih.gov/blast/db/ webcitenr

redund

REDUND

redundb

List of complete genomes (flat file)

http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/slritools/slri/seqhound/genomes/chromff webcite

chrom

CHROM

gendb

ASN.1 for complete genomes

ftp://ftp.ncbi.nih.gov/genomes/ webcite*/*.asn

comgen

TAXGI, ACCDB

gendb

Taxonomy release (flat file)

ftp://ftp.ncbi.nih.gov/pub/taxonomy/ webcitetaxdump.tar

importtaxdb

TAX, GCODE, DIV, DEL, MERGE

taxdb

ASN.1 MMDB release

ftp://ftp.ncbi.nih.gov/mmdb/mmdbdata/ webcite*.val

cbmmdb

MMDB, MMGI

strucdb

MMDB (database table)

MMDB table

vastblst

DOMDB

strucdb

3-D chain BLAST sets (flat file)

ftp://ftp.ncbi.nih.gov/mmdb/nrtable/ webcitenrpdb.*

pdbrep

DOMDB

strucdb

FASTA nr database

ftp://ftp.ncbi.nih.gov/blast/db/ webcitenr

nblast

nrB

neigdb

BLAST ASN.1 results

nrB table available nrB and nrN tables availables at ftp://ftp.mshri.on.ca/pub/NBLAST webcite

nbraccess

nrN

neigdb

LL_tmpl (flat file)

ftp://ftp.ncbi.nih.gov/refseq/LocusLink/ webciteLL_tmpl

llparser

LL_OMIM, LL_GO, LL_LLINK, LL_CDD

lldb

gene_associaton.com pugen.GenBank/Swissprot (flat files)

http://www.geneontology.org webcite

addgoid

LL_GO

lldb

function.ontology process.ontology component.ontology (flat files)

http://www.geneontology.org webcite

goparser

GO_PARENT, GO_NAME, GO_REFERENCE, GO_SYNONYM

godb

CDD database

ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/ webcite

domname

DOMNAME

rpsdb

FASTA nr database and CDD database

ftp://ftp.ncbi.nih.gov/blast/db/ webcitenr; ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/ webcite DOMNAME and RPSDB tables available at ftp://ftp.mshri.on.ca/pub/RPS webcite

rpsdb

RPSDB

rpsdb


Michalickova et al. BMC Bioinformatics 2002 3:32   doi:10.1186/1471-2105-3-32

Open Data