<owner_name="James Knight, knight@cs.ucdavis.edu">
SEQIO -- A Package for Sequence File I/O

# BIOSEQ.TXT - An Example BIOSEQ File

    #
    # bioseq.txt - BIOSEQ entries for various databases (Version 1.2)
    #
    # This file contains BIOSEQ entries for a number of databases.  Currently,
    # there are entries for GenBank, GenPept (part of GenBank), NRFES, NRL3D,
    # PIR, PROSITE, REPBASE, SWISS-PROT and UTR (part of NRFES).
    #
    # To customize it for your installation, go through the entries and for
    # each entry:
    #      1) Change the root directory from "/databases/..." to the
    #         directory where you have installed that database's files.
    #     2a) If one of the choices listed in the entry matches your database
    #         file organization, uncomment the file/alias lines (if they
    #         have been commented).
    #     2b) If your installation differed from the choices listed in the
    #         entry, comment out any uncommented lines, add the names of
    #         the database's files, and rewrite the aliases.
    #      3) Comment out (or change the name of) any index files you don't
    #         want to use.  Only include the index files for the identifiers
    #         you want the users to be able to access entries by.
    #      4) Run idxseq for each of the databases to create the index files.
    #
    # In this version, only a few databases are given, but my hope is that
    # this file could become a canonical list of the databases, their
    # ftp/WWW locations or ordering information, and their file structure.
    # So, if you administer, or are familiar with, a database which either
    # is not included here, is incorrectly given here, or occurs in an ftp
    # site, CD-ROM or floppy disk release with another file structure,
    # please send e-mail to knight@cs.ucdavis.edu.
    #

    #
    # Virtual BIOSEQ entries used to create and store index files for
    # the NID and PID identifiers  (to give random access to entries
    # using the "nid" and "pid" identifiers).
    #

    >NID
    >IdPrefix: nid
    >Index: /databases/nididx

    >PID
    >IdPrefix: pid
    >Index: /databases/pididx

    #
    # The EMBL Nucleotide Sequence Database
    #
    >EMBL:  /databases/embl
    >Name:  EMBL
    >IdPrefix: embl
    >Index: emblindex
    >Format: emblfast
    >Alphabet:  DNA
        #
        # EMBL files as found at ftp site ftp.ebi.ac.uk in
        # /pub/databases/embl/release.
        #
        est?.dat, fun.dat, hum?.dat, inv.dat, mam.dat, org.dat, patent.dat,
        phg.dat, pln.dat, pro.dat, rod.dat, sts.dat, syn.dat, unc.dat
        vrl.dat, vrt.dat

        est:(est?.dat),  est1:(est1.dat),  est2:(est2.dat),  est3:(est3.dat),
        est4:(est4.dat),  est5:(est5.dat),  est6:(est6.dat),  fun:(fun.dat),
        hum:(hum?.dat),  hum1:(hum1.dat),  hum2:(hum2.dat),  inv:(inv.dat),
        mam:(mam.dat),  org:(org.dat),  pat:(patent.dat),  patent:(patent.dat),
        phg:(phg.dat),  pln:(pln.dat),  pri:(pri.dat),  pro:(pro.dat),
        rod:(rod.dat),  sts:(sts.dat),  syn:(syn.dat),  unc:(unc.dat),
        vrl:(vrl.dat),  vrt:(vrt.dat)

    #
    # The ENZYME Database
    #
    >enzyme:  /databases/enzyme
    >Name: ENZYME
    >IdPrefix: ec
    >Index: ecindex
    >Format: EMBL
        #
        # Enzyme files as found at ftp site ncbi.nlm.nih.gov in /repository/enzyme.
        #
        enzyme.dat

    #
    # The GenBank Flat-File Database
    #
    >GenBank,gb:  /databases/genbank
    >Name:  GenBank
    >IdPrefix:  gb
    >Index: gbindex
    >Format:  gbfast
    >Alphabet:  DNA
        #
        # GenBank files as found at ftp site ncbi.nlm.nih.gov in /genbank.
        # Uncomment one of the alternatives for the between-release, daily
        # files (if you have those files).
        #
        gbbct.seq, gbest?.seq, gbinv.seq, gbmam.seq, gbpat.seq, gbphg.seq
        gbpln.seq, gbpri.seq, gbrna.seq, gbrod.seq, gbsts.seq, gbsyn.seq,
        gbuna.seq, gbvrl.seq, gbvrt.seq

        bct:(gbbct.seq), est:(gbest?.seq), est1:(gbest1.seq), est2:(gbest2.seq)
        est3:(gbest3.seq), est4:(gbest4.seq), est5:(gbest5.seq)
        est6:(gbest6.seq), est7:(gbest7.seq), inv:(gbinv.seq),  mam:(gbmam.seq)
        pat:(gbpat.seq), phg:(gbphg.seq), pln:(gbpln.seq), pri:(gbpri.seq)
        rna:(gbrna.seq), rod:(gbrod.seq), sts:(gbsts.seq), syn:(gbsyn.seq)
        una:(gbuna.seq), vrl:(gbvrl.seq), vrt:(gbvrt.seq)
        ~bct:(gbbct.seq), ~est:(gbest?.seq), ~inv:(gbinv.seq),  ~mam:(gbmam.seq)
        ~pat:(gbpat.seq), ~phg:(gbphg.seq), ~pln:(gbpln.seq),  ~pri:(gbpri.seq)
        ~rna:(gbrna.seq), ~rod:(gbrod.seq), ~sts:(gbsts.seq),  ~syn:(gbsyn.seq)
        ~una:(gbuna.seq), ~vrl:(gbvrl.seq), ~vrt:(gbvrt.seq)

        # daily/gbcu.flat,  daily:(daily/gbcu.flat)
        # daily-nc/nc????.flat,  daily:(daily-nc/nc????.flat)

    #
    # The GenPept Protein Translation of GenBank coding sequences.
    #
    >GenPept:  /databases/genbank
    >Name:  GenPept
    >IdPrefix:  gp
    >Index: genpeptindex
    >Format:  FASTA
    >Alphabet:  Protein
        #
        # GenPept files as found at ftp site ncbi.nlm.nih.gov in /genbank
        #
        genpept.fsa, daily/gpcu.fsa

    #
    # The Non-Redundant Functionally Equivalent Sequences (NRFES) Database.
    #
    >NRFES:  /databases/NRFES
    >Name:  NRFES
    >IdPrefix:  gb
    >Index: nrfesindex
    >Format:  NBRF
    >Alphabet:  DNA
        #
        # NRFES files as found at ftp site ncbi.nlm.nih.gov in /repository/NRFES.
        #
        all_v05/(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
        cds_v05/(bctc, invc, mamc, orgc, phgc, plnc, pric, rodc, vrlc, vrtc, yeac)
        exo_v05/(inve, mame, orge, plne, prie, rode, vrle, vrte, yeae)
        ivs_v05/(invi, mami, orgi, plni, prii, rodi, vrli, vrti, yeai)

        ~:(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
        all:(bcta, inva, mama, orga, phga, plna, pria, roda, vrla, vrta, yeaa)
        cds:(bctc, invc, mamc, orgc, phgc, plnc, pric, rodc, vrlc, vrtc, yeac)
        exo:(inve, mame, orge, plne, prie, rode, vrle, vrte, yeae)
        ivs:(invi, mami, orgi, plni, prii, rodi, vrli, vrti, yeai)

        bct:(bcta), inv:(inva), mam:(mama), org:(orga), phg:(phga), pln:(plna)
        pri:(pria), rod:(roda), vrl:(vrla), vrt:(vrta), yea:(yeaa)

    #
    # The NRL_3D Protein Sequence--Structure Database (a mirror of the PDB
    # database in PIR/CODATA file format).
    #
    >NRL3D:  /databases/pir
    >Name:  NRL3D
    >IdPrefix:  pdb
    >Index: nrl3dindex
    >Format:  pirfast
    >Alphabet:  Protein
        #
        # NRL_3D files as included in the PIR release found at ftp site
        # ncbi.nlm.nih.gov in /repository/PIR.
        #
        nrl3d.dat

    #
    # The Protein Information Resource (PIR) Database.
    #
    >PIR:  /databases/pir
    >Name:  PIR
    >IdPrefix:  pir
    >Index: pirindex
    >Format:  pirfast
    >Alphabet:  Protein
        #
        # PIR files as found at ftp site ncbi.nlm.nih.gov in /repository/PIR.
        #
        pir1.dat, pir2.dat, pir3.dat pir4.dat

        ~1:(pir1.dat), ~2:(pir2.dat), ~3:(pir3.dat), ~4:(pir4.dat)
        ~12:(pir1.dat,pir2.dat), ~13:(pir1.dat,pir3.dat), ~23:(pir2.dat,pir3.dat)
        ~123:(pir1.dat,pir2.dat,pir3.dat)

    #
    # The PROSITE Pattern Database.
    #
    >PROSITE:  /databases/prosite
    >Name:  PROSITE
    >IdPrefix:  pros
    >Index: prositeindex
    >Format: EMBL
        #
        # PROSITE files as found at ftp site ncbi.nlm.nih.gov in
        # /repository/prosite.
        #
        prosite.dat

    #
    # The REPBASE Repetitive Element Database.
    #
    >repbase:  /databases/repbase
    >Name:  REPBASE
    >IdPrefix:  rpb
    >Index: repbaseindex
    >Format:  EMBL
        #
        # REPBASE files as found at ftp site ncbi.nlm.nih.gov in
        # /repository/repbase.
        #
        MAIN/(B1.rodent, B2.rodent, L1.primate, MIR.mammal, MIR.primate,
              MIR.rodent, MIR2.primate, THE.mammal, THE.primate, THE.rodent,
              THR.human, alu.galago, alu.human, alu.other)
        MER/MER*.pri
        REF/(humrep.ref, invrep.ref, mamrep.ref, plnrep.ref, rodrep.ref,
             simple.ref, vertrep.ref)

        B1:(B1.rodent), B2:(B2.rodent), L1:(L1.primate)
        MIR:(MIR.mammal, MIR.primate, MIR.rodent), MIR2:(MIR2.primate)
        THE:(THE.mammal, THE.primate, THE.rodent), THR:(THR.human)
        alu:(alu.galago, alu.human, alu.other)
        rodent:(B1.rodent, B2.rodent, MIR.rodent),
        rod:(B1.rodent, B2.rodent, MIR.rodent),
        primate:(L1.primate, MIR.primate, MIR2.primate, THE.primate)
        pri:(L1.primate, MIR.primate, MIR2.primate, THE.primate)
        mammal:(MIR.mammal, THE.mammal), mam:(MIR.mammal, THE.mammal)
        human:(THR.human, alu.human)

    #
    # The SWISS-PROT Protein Sequence Data Bank.
    #
    >SWISS-PROT,swissprot,sprot:  /databases/swiss-prot
    >Name:  SWISS-PROT
    >IdPrefix:  sp
    >Index: sprotindex
    >Format:  spfast
    >Alphabet:  Protein
        #
        # SWISS-PROT files as found at ftp site ncbi.nlm.nih.gov in
        # /repository/swiss-prot.  The ?? match the release number of
        # the database.
        #
        sprot??.dat

        #  updates/new-seq.dat

    #
    # The UTR Database (UnTRanslated regions of protein coding genes).
    #
    >UTR:  /databases/NRFES/utr
    >Format: FASTA
    >Index: utrindex
    >Alphabet: DNA
        #
        # UTR files as included in the NRFES release found at ftp site
        # ncbi.nlm.nih.gov in /repository/NRFES/utr.
        #
        amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p
        mou_3p, nema_3p, prot_3p, rat_3p
        amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p
        mou_5p, nema_5p, prot_5p, rat_5p

        ~_3p:(amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p,
              mou_3p, nema_3p, prot_3p, rat_3p)
        ~_5p:(amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p,
              mou_5p, nema_5p, prot_5p, rat_5p)
        3p:(amp_3p, bird_3p, dro_3p, fish_3p, inse_3p, mam_3p, mollu_3p,
            mou_3p, nema_3p, prot_3p, rat_3p)
        5p:(amp_5p, bird_5p, dro_5p, fish_5p, inse_5p, mam_5p, mollu_5p,
            mou_5p, nema_5p, prot_5p, rat_5p)
        amp:(amp_3p,amp_5p), bird:(bird_3p,bird_5p), dro:(dro_3p,dro_5p)
        fish:(fish_3p,fish_5p), inse:(inse_3p,inse_5p), mam:(mam_3p,mam_5p)
        mollu:(mollu_3p,mollu_5p), mou:(mou_3p,mou_5p), nema:(nema_3p,nema_5p)
        prot:(prot_3p,prot_5p), rat:(rat_3p,rat_5p)