# embossrc (without SRS database)

# For setting up following databases, please download this file
# and save as "~/.embossrc" on your home directory.

# By default EMBOSS is installed at /usr/local but the directory can
# be changed with --prefix when you configure EMBOSS.

# SET emboss_acdroot $YOUR_PREFIX/share/EMBOSS/acd
# SET embossdata     $YOUR_PREFIX/share/EMBOS/data

SET emboss_acdroot /usr/local/share/EMBOSS/acd
SET emboss_data /usr/local/share/EMBOSS/data

# Nucleotide
DB embl [ 
  type: N 
  format: embl 
  method: url
  dbalias: EMBL
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL-all:'%s']+-ascii+1"
  comment: "Database of nucleotide sequence in Europe."
]

DB genbankn [
  type: N
  format: genbank
  method: url
  url: "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=gb&retmode=text&id=%s"
  dbalias: GENBANKN
  comment: "The NIH genetic sequence database, an annotated collection of all publicly
            available DNA sequences."
]

DB refseqn [
  type: N 
  format: genbank
  method: url
  dbalias: REFSEQN
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[REFSEQGENREL:'%s']+-ascii+1"
  comment: "Database providing non-redundant curated data representing knowledge of known genes."
]

DB ddbj [
  type: N
  format: genbank
  method: url
  dbalias: DDBJ
  fields: "sv des org key"
  url: "http://xml.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=%s"
  comment: "Database of nucleotide sequence in Japan."
]

DB fantom2 [
  type: N
  format: fasta
  method: url
  dbalias: FANTOM2
  fields: "des"
  url: "http://fantom2.gsc.riken.jp/db/annotate/seqview.cgi?type=cdnaseq&masterid=%s"
  comment: "Functional Annotation of the Mammalian Genome (FANTOM) 2"
]

DB fantom3 [
  type: N
  format: fasta
  method: url
  dbalias: FANTOM3
  fields: "des"
  url: "http://fantom3.gsc.riken.jp/db/reference/content.cgi?category=dnaseq&masterid=%s"
  comment: "Functional Annotation of the Mammalian Genome (FANTOM) 3"
]

# Protein
DB uniprotkb [
  type: P 
  format: swiss
  method: url
  dbalias: UNIPROTKB
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[UNIPROT-all:'%s']+-vn+2+-ascii"
  comment: "The central hub for the collection of functional information on proteins,
            with accurate, consistent and rich annotation."
]

DB refseqp [ 
  type: P 
  format: genbank
  method: url
  dbalias: REFSEQP
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[REFSEQP:'%s']+-ascii"
  comment: "Database of protein information from REFSEQ."
]

DB genbankp [
  type: P 
  format: genbank
  method: url
  dbalias: GENBANKP
  url: "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&rettype=gb&retmode=text&id=%s"
  comment: "Database of protein information from GENBANK"
]

DB swissprot [
  type: P 
  format: swiss
  method: url
  dbalias: SWISSPROT
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWISSPROT-all:'%s']+-vn+2+-ascii"
  comment: "Database of protein sequences produced collaboratively by the Swiss
            Institute for Bioinformatics (SIB) and the European Bioinformatics
            Institute (EBI)."
]

DB swall [
  type: P 
  format: swiss
  method: url
  dbalias: SWALL
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWALL-all:'%s']+-vn+2+-ascii"
  comment: "A combined database of Swiss-Prot, SPTREMBL and TREMBLNEW. Does not contain REMTREMBL."
]

DB sw [
  type: P
  format: swiss
  method: url
  dbalias: SW
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWALL-all:'%s']+-vn+2+-ascii"
  comment: "A combined database of Swiss-Prot, SPTREMBL and TREMBLNEW. Does not contain REMTREMBL."
]

DB uniparc [
  type: P
  format: swiss
  method: url
  dbalias: UNIPARC
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[UNIPARC:'%s']+-ascii+-view+UniParc2Flat"
  comment: "A comprehensive and non-redundant database that contains most of the publicly available protein sequences."
]

DB pir [ 
  type: P 
  format: pir
  method: url
  dbalias: PIR
  fields: "sv des org key"
  url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[PIR:'%s']+-ascii"
  comment: "Protein Identification Resource."
]

# SET emboss_proxy "10.3.1.1:8080"