<opt 
  name="blastfiles"
  date="20040821"
  
  blasthome="${ARGOS_ROOT}/common/servers/blast/Bin" 
  formatdb="${ARGOS_ROOT}/common/servers/blast/Bin/formatdb" 
  formatdbopts="-o F " 
  isprot_patt="(translation|aa_)"
  >
  
  <title>Blast index writer</title>
  <about>
    These are configurations for updating blast indices,
    rc files, html pages, given genome fasta input files
    and fasta/feature groups.
  </about>
  
  <informat>fasta</informat>  
  <outformats>ncbi</outformats>
  <outformats> </outformats>

  <!-- feature sets to make blast indices -->
  <blastset>gene</blastset>
  <blastset>transcript</blastset>
  <blastset>translation</blastset>
  <blastset>ncRNA</blastset>
<!--   <blastset>transposon</blastset> -->
  <blastset>pseudogene</blastset>
  <blastset>intergenic</blastset>
  <blastset>scaffold</blastset>
  <blastset>chromosome</blastset>
  <blastset>syntenic_region</blastset>
<!-- need aliases or consensus feature names here: 
    golden_path_fragment/databank_scaffold/scaffold/supercontig
    chromosome/golden_path/ultracontig
-->

  
  <doc id="dbrc" path="blast/blast.rc"><![CDATA[
# blast.rc 
# This is dynamic configuration file for NCBI WWW BLAST service
#
# Number of CPUs to use for a single request
#
NumCpuToUse     1
#
# Here are list of combinations program/database, 
# that allowed by BLAST service. Format: <program> <db> <db> ...
#
blastn  
blastp 
blastx 
tblastn 
tblastx 
  ]]></doc>
  
  
  
  <!-- also need to write some .nal, .pal ncbi blast files  to join other dbs 
    .. put tag into individual ones to join, eg. nalfile="na_all na_est"
  -->
  
  <doc id="dbselect" path="blast/blastdb.in">
  <!-- database <select> include file html; no content tag here -->
  <!-- change this to be entire blast html form instead of using shtml #include ? -->
  <header title=""><![CDATA[ ]]></header>
  <footer title=""><![CDATA[ ]]></footer>
  </doc>
 
 
 
  <doc id="dbtable" path="blast/blast_databases.html">
  <!-- no content tag here -->
  <!-- optional <tableheader> four fields are dbname, dbfile, update-date, description -->
  <header title=""><![CDATA[<HTML>
  <HEAD>
  <TITLE>${species} BLAST Databases</TITLE> 
  </HEAD>
  
  <BODY>  
  <h1>
  <I>${species}</I> Genome BLAST
  </h1>
  <h2>
  Data release <a href="${release_url}">${rel}</a>
  <br>Data sets for BLAST search
  </h2>
  <HR>
  <B><LI>Database</B> - Choose a database &nbsp &nbsp <FONT COLOR="red"><B>required</B></FONT>
  <BR><BR>
  <TABLE BORDER=1 cellpadding="5" cellspacing="1">
  ]]></header>
  
  <footer title=""><![CDATA[
  <TR> 
  <TD colspan=4 align=left> <a name=key> <B>key: AA = protein, NT = nucleotide. 
  To download databases, visit the  <A HREF="/annot/" target=_self>Sequence 
  Download Page</A></B> </TD>
  </TR>
  </TABLE>
  </BODY>
  </HTML>
  ]]></footer> 
  </doc>

   <!-- these db entries for databases.html -->
   <!-- want sorted in given order; as array not hash -->
   <!-- FIXME: $org name ... -->
   
  <blastdb id="na_all" title="  All ${species} sequences (NT)"><![CDATA[
    Euchromatin,  heterochromatin, and predicted genes; 
    genomic clones, ESTs, STSs, P-element 
    insertion sites, and public sequences from GenBank (see below)
  ]]>
  </blastdb> 

    <!-- these are generic for any organism -->
  <blastdb id="chromosome" title="  All ${species} genome chromosome arms (NT)"
      nalfile="na_all"
  ><![CDATA[  
    Whole genome by chromosome arms
  ]]>
  </blastdb> 

  <blastdb id="transcript" title="  Predicted ${species} genes (NT)"
    nalfile="na_all"
    ><![CDATA[
    Complete transcript (CDS + UTR) for all of the genes 
   ]]>
  </blastdb> 

  <blastdb id="translation" title="  Predicted ${species} proteins (AA)"><![CDATA[
    Peptide translations for all of the genes 
  ]]>
  </blastdb> 

  <!-- fixme; need to extract scaffold dna from chado db -->
  <blastdb id="golden_path" old_name="scaffold"
    title=" Euchromatin and heterochromatin ${species} scaffolds (NT)"
    nalfile="na_all"
    ><![CDATA[
    Genomic sequence for the euchromatic chromosome arms, 
     and from the heterochromatin assembly,
     divided into ~350kb GenBank scaffolds 
  ]]>
  </blastdb> 

  <blastdb id="intergenic" title="Intergenic ${species} sequence (NT)"
    nalfile="na_all"
    ><![CDATA[
  Intergeneic regions -- genome sequence between genes  
  ]]>
  </blastdb> 

 <blastdb id="transposon" skip="1" title="Transposon insertions (NT)"><![CDATA[
  Transposon insertion sites in genome 
  ]]>
  </blastdb> 



  <!-- these are flybase specific -->
  
  <blastdb id="na_cDNA" title=" BDGP full-length cDNAs (NT)"
    nalfile="na_all" org="dmel"
    ><![CDATA[
  <I>${species}</I> full-length cDNAs from the BDGP
  ]]>
  </blastdb> 

  <blastdb id="na_geno_clones" title=" BDGP/EDGP genomic clones (NT)"
    nalfile="na_all"  org="dmel"
    ><![CDATA[
  P1, BAC, and cosmid sequences from the BDGP & EDGP that have been submitted 
        to GenBank -- this does not include whole genome shotgun sequence 
  ]]>
  </blastdb> 


<!--   <blastdb id="dmel_hetero_scaffolds" title=" Heterochromatin scaffolds (NT)"><![CDATA[ -->
<!--   Genomic sequence from <a href="http://www.celera.com" target="_self">Celera</a>  -->
<!--         for the heterochromatin from the WGS3 assembly -->
<!--   ]]> -->
<!--   </blastdb>  -->

 
  <blastdb id="dmel_aa_swall" title=" SwissProt and TREMBL proteins (SWALL) (AA)"><![CDATA[
  A non-redundant combination of the <i>${species}</i> entries from the 
        SwissProt+TrEMBL+TrEMBLNew databases (SWALL)
  ]]>
  </blastdb> 
  
  <blastdb id="dmel_aa_uniprot" title=" UniProt proteins (AA)"><![CDATA[
  <i>${species}</i> proteins from UniProt
  ]]>
  </blastdb> 
  
  <blastdb id="dmel_aa_refseq" title=" RefSeq proteins (AA)"><![CDATA[
  <i>${species}</i> proteins from  RefSeq
  ]]>
  </blastdb> 

  <blastdb id="dmel_na_refseq" title=" RefSeq Sequences (NT)"><![CDATA[
  <i>${species}</i> nucleic sequences from  RefSeq
  ]]>
  </blastdb>
  
  <blastdb id="na_gb" title=" GenBank (without BDGP, EDGP, Celera or dbEST) (NT)"
      nalfile="na_all"
  ><![CDATA[
   <i>${species}</i> sequences collected from public sequence databases 
        (but without BDGP, EDGP, Celera, or dbEST sequences)
  ]]>
  </blastdb> 

  <blastdb id="na_est" title="ESTs from BDGP and dbEST cDNAs (NT)" org="dmel" ><![CDATA[
   <I>Drosophila</I> Expressed Sequence Tags from the BDGP and from dbEST 
        cDNAs (redundant)
  ]]>
  </blastdb> 

  <blastdb id="na_EST" part_of="na_est" title="" skip="1"
    nalfile="na_all na_est"
  ><![CDATA[
   Expressed Sequence Tags
  ]]>
  </blastdb> 
  <blastdb id="na_dbEST" part_of="na_est" title="" skip="1"
    nalfile="na_all na_est"
    ><![CDATA[
  dbEST  cDNAs
  ]]>
  </blastdb> 
  
  <blastdb id="na_pe" title=" P element insertion sites (NT)" nalfile="na_all" org="dmel"><![CDATA[
  Genomic sequence flanking BDGP P-element insertions (BDGP)
  ]]>
  </blastdb> 

  <blastdb id="na_re" title=" Repeats (NT)"  nalfile="na_all" ><![CDATA[
  a curated set of <i>${species}</i> known repeats
  ]]>
  </blastdb> 

  <blastdb id="na_STS" title=" STSs (NT)"  nalfile="na_all"><![CDATA[
   <I>Drosophila</I> STSs from the BDGP and EDGP mapping projects 
  ]]>
  </blastdb> 
 
 <blastdb id="na_te" title=" Transposons (NT)" nalfile="na_all"><![CDATA[
  a curated set of <i>${species}</i> transposable elements 
  ]]>
  </blastdb> 


</opt>
