Index: src/hg/archaeStuff/data/Genome-info-euk
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-euk,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 1000000 -r1.17 -r1.18
--- src/hg/archaeStuff/data/Genome-info-euk	2 Jul 2009 16:46:36 -0000	1.17
+++ src/hg/archaeStuff/data/Genome-info-euk	1 Feb 2010 11:06:25 -0000	1.18
@@ -1,381 +1,381 @@
 ## Genome-info-euk - only add fields which you wish to over-ride in Genome-info-db (automatically 
 ##                    generated using "make-genome-info" perl script).
 #
 # Description of Fields for each genome entry:
 # 
 # Org_abr: first four letters of genus & species, plus strain identifier (if any)
 #  NOTE: Org_abr *must* occur prior to any of the fields given below to be associated 
 #        with the right genome!
 # Org_name: Species name (no length restriction -- taken from NCBI directory name; 
 #            should NOT be changed)
 # Menu_name: Species name preferred in pull-down menu (usually a shortenned version
 #             of Org_name -- i.e. without strain; should still be unique)
 # Domain:  Domain (Bacteria, Archaea, or Eukarya)
 # DB_name: name used for species database in mysql
 # Cent_DB: Production central database which must be set to same value as variable
 #              "central.db" in hg.conf in cgi-bin directory; will use a default value if not set explicitly
 # DB_src: Source of information for genome DB which determines the format of information
 #          input into genome browser;  defalt value "NCBI"; alt vals: "JGI", etc.; 
 #          will use default if not set explicitly
 # Tax_name: Full name of species (including strain) (normally taken from NCBI Genbank files)
 # Tax_ID:  NCBI's unique species identifier used in its taxonomy classification
 # Dom_ct:  Domain count -- priority order in which you want it displayed in the browser;c
 #          can put an integer, or assign same priority as another organism (allows floating to stay
 #           in correct place for unpublished genomes) using notation '&Org_abbr' i.e. (Dom_ct: &Heli_pylo_J99)
 # Gen_ID:  Genome unique ID number used to access organim's genome page at NCBI
 # Pub_id: Pubmed identifier for publication describing genome sequence
 # Seq_acc: List of accession numbers for all refseq (NC*) genome files
 # Name_chg: Name mapping for each genome sequence file in pairs (i.e. NC2001 chr1 NC2002 chr2 ..etc)
 # Seq_size: Size of sequences, in same order as names in Seq_acc:
 # Gene_ct: Gene count list, separated by spaces, in order of seqs in Seq_acc field
 # Multiz: track abbreviation, followed by list of organisms (db names) to be aligned in multiz or blastz track
 # Public_multiz: track abbreviation, followed by list of organisms (db names) to be aligned in multiz or blastz track (used in public browser)
 # Phylo: phylogenetic tree string used to construct phylohmm track i.e. (org1,(org2,org3))
 # Rel_date: Release date for current sequence version of genome, read from NCBI's microbial genomes page
 # Sp_info: Optional sentences about species included in description.html front page (no length 
 #          restriction, but no newlines allowed)
 # Seq_src: Sequencing center that submitted the genome sequence (also from NCBI's microbial genomes page)
 # Web_seq: web/ftp address for fasta/genbank sequence files
 # Web_db:  NCBI web address for this organism's genome
 # Trna_opt: tRNAscan-SE options to use in auto-runs
 # Trna_abr: tRNAscan-SE output files prefix
 # Gen_seq: location of local FASTA genome sequence file
 # Prot_seq: location of local copy of protein sequences
 # Feat_seq: All features in genome file (including protein genes, ncRNA genes, intergenic 
 #           regions), separated into individual fasta seqs
 
 Org_abr: Hsapi
 Org_name: Homo sapiens (hg18 - NCBI Build 36.1 Mar 2006)
 Domain:  Eukaryota
 DB_name: hg18
 Tax_ID:  9606: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#human
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg18
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: hg18-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/hg18/hg18-genome.fa
 Sprinzl: 999
 
 Org_abr: Hsapi19
 Org_name: Homo sapiens (hg19 - NCBI Build 37.1 Feb 2009)
 Domain:  Eukaryota
 DB_name: hg19
 Tax_ID:  9606: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#human
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg19
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: hg19-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/hg19/hg19-genome.fa
 Sprinzl: 999
 
 Org_abr: Ptrog
 Org_name: Pan troglodytes (chimp) (Mar 2006)
 Domain:  Eukaryota
 DB_name: panTro2
 Tax_ID:  9598: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pan.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#chimp
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chimp&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: panTro2-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/panTro2/panTro2-genome.fa
 Sprinzl: 999
 
 Org_abr: Ppygm_abel
 Org_name: Pongo pygmaeus abelii (orangutan) (July 2007)
 Domain:  Eukaryota
 DB_name: ponAbe2
 Tax_ID:  9601: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Pongo.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#orangutan
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chimp&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: ponAbe2-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/ponAbe2/ponAbe2-genome.fa
 
 Org_abr: Mmusc
 Org_name: Mus musculus (mm9 July 2007)
 Domain:  Eukaryota
 DB_name: mm9
 Tax_ID:  10090: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#mouse
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Mouse&db=mm9
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: mm9-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/mm9/mm9-genome.fa
 Sprinzl: 933
 
 Org_abr: Rnorv
 Org_name: Rattus norvegicus (rn4 Nov 2004)
 Domain:  Eukaryota
 DB_name: rn4
 Tax_ID:  10116: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Rattus.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#rat
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Rat&db=rn4
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: rn4-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/rn4/rn4-genome.fa
 Sprinzl: 933
 
 Org_abr: Cfami
 Org_name: Canis familiaris (dog) (May 2005)
 Domain:  Eukaryota
 DB_name: canFam2
 Tax_ID:  9615: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Caniformia; Canidae; Canis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#dog
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Dog&db=canFam2
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: canFam2-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/canFam2/canFam2-genome.fa
 Sprinzl: 999
 
 Org_abr: Fcatu
 Org_name: Felis catus (cat) (Broad Release 3 May 2005)
 Domain:  Eukaryota
 DB_name: felCat3
 Tax_ID:  9685: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Felinae; Felis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#cat
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Cat&db=felCat3
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: felCat3-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/felCat3/felCat3-genome.fa
 
 Org_abr: Btaur
 Org_name: Bos taurus (cow) (Baylor release Btau_4.0 Oct 2007)
 Domain:  Eukaryota
 Tax_ID:  9913: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#cow
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Cow&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: bosTau4-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/bosTau4/bosTau4-genome.fa
 
 Org_abr: Ggall
 Org_name: Gallus gallus (galGal3 May 2006)
 Domain:  Eukaryota
 DB_name: galGal3
 Tax_ID:  9031: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#chicken
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chicken&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: galGal3-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/galGal3/galGal3-genome.fa
 
 Org_abr: Mmula
 Org_name: Macaca mulatta (Rhesus Jan 2006)
 Domain:  Eukaryota
 Tax_ID:  9544: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#rhesus 
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgGateway?org=Rhesus&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: rheMac2-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/rheMac2/rheMac2-genome.fa
 
 Org_abr: Ecaba
 Org_name: Equus caballus (horse) (Jan 2007)
 Domain:  Eukaryota
 DB_name: equCab1
 Tax_ID:  9796: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Perissodactyla; Equidae; Equus.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#horse
 Web_db:  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Horse&db=0
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: equCab1-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/equCab1/equCab1-genome.fa
 
 Org_abr: Dreri
 Org_name: Danio rerio (Zebrafish) (Zv8 Apr 2009)
 Domain:  Eukaryota
 DB_name: danRer_v8
 Tax_ID:  7955: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Cyprinidae; Danio.
 Web_seq: ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv8release/
 Web_db:  http://www.sanger.ac.uk/Projects/D_rerio/Zv8_assembly_information.shtml
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: danRer_v8-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/danRer_v8/danRer_v8-genome.fa
 
 Org_abr: Frubr
 Org_name: Takifugu rubripes (fr2 Oct 2004) 
 Domain:  Eukaryota
 DB_name: fr2
 Tax_ID:  31033: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei; Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes; Tetradontoidea; Tetraodontidae; Takifugu.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#fugu
 Web_db:  http://genome.jgi-psf.org/fugu6/fugu6.info.html
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: fr2-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/fr2/fr2-genome.fa
 
 Org_abr: Dmela
 Org_name: Drosophila melanogaster (Release 5 Apr 2006)
 Domain:  Eukaryota
 DB_name: dm3
 Tax_ID:  7227: Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora.
 Web_seq: http://www.fruitfly.org/sequence/release5genomic.shtml
 Web_db:  http://www.fruitfly.org/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: dm3-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/dm3/dm3-genome.fa
 Sprinzl: 924
 
 Org_abr: Celeg
 Org_name: Caenorhabditis elegans (Jan 2007)
 Domain:  Eukaryota
 DB_name: ce4
 Tax_ID:  6239: Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#c_elegans
 Web_db:  http://www.wormbase.org/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: ce4-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/ce4/ce4-genome.fa
 Sprinzl: 920
 
 Org_abr: Cbrig
 Org_name: Caenorhabditis briggsae (cb3 Jan 2007)
 Domain:  Eukaryota
 DB_name: cb3
 Tax_ID:  6238: Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#c_briggsae
 Web_db:  http://www.wormbase.org/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: cb3-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/cb3/cb3-genome.fa
 Sprinzl: 920
 
 Org_abr: Cbren
 Org_name: Caenorhabditis brenneri (Jan 2007)
 Domain:  Eukaryota
 DB_name: caePb1
 Tax_ID:  135651: Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#caePb
 Web_db:  http://www.wormbase.org/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: caePb1-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/caePb1/caePb1-genome.fa
 
 Org_abr: Crema
 Org_name: Caenorhabditis remanei (Mar 2006)
 Domain:  Eukaryota
 DB_name: caeRem2
 Tax_ID:  31234: Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis.
 Web_seq: http://hgdownload.cse.ucsc.edu/downloads.html#caeRem
 Web_db:  http://www.wormbase.org/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: caeRem2-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Euk/caeRem2/caeRem2-genome.fa
 
 Org_abr: Spurp
 Org_name: Strongylocentrotus purpuratus (Sea urchin) (Version 2.1)
 Domain:  Eukaryota
 Tax_ID:  7668: Eukaryota; Metazoa; Echinodermata; Eleutherozoa; Echinozoa; Echinoidea; Euechinoidea; Echinacea; Echinoida; Strongylocentrotidae; Strongylocentrotus.
 Web_seq: ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/fasta/Spur_v2.1/
 Web_db:  http://www.hgsc.bcm.tmc.edu/projects/seaurchin/
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: Spurp-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/Spurp/Spurp-genome.fa
 
 Org_abr: Athal
 Org_name: Arabidopsis thaliana (Feb 2004)
 Domain:  Eukaryota
 Tax_ID:  3702: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
 Web_seq: ftp://ncbi.nlm.nih.gov/genbank/genomes/A_thaliana/
 Web_db:  http://www.arabidopsis.org/
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: Athal-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Arabidopsis_thaliana/Athal-genome.fa
 Sprinzl: 851
 
 Org_abr: Mtrun
 Org_name: Medicago truncatula (March 2009 Version 3.0)
 Domain:  Eukaryota
 Tax_ID:  3880: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago.
 Web_seq: http://www.cis.udel.edu/~alvaro/Medicago_ver3_Fasta/
 Web_db:  http://medicago.org/genome/
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: mt3-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/mt3/mt3-genome.fa
 
 Org_abr: Gmax
 Org_name: Glycine max (soybean) (Glyma0 preliminary release)
 Domain: Eukaryota
 Tax_ID:  3847: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine.
 Web_seq: ftp://ftp.jgi-psf.org/pub/JGI_data/Glycine_max/assembly/
 Web_db:  http://www.phytozome.net/soybean
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: glyMa0-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/glyMa0/glyMa0-genome.fa
 
 Org_abr: Ptric
-Org_name: Populus trichocarpa (June 2004 Version 1.0)
+Org_name: Populus trichocarpa (Jan 2010 Version 2.0)
 Domain: Eukaryota
 Tax_ID:  3694: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Malpighiales; Salicaceae; Saliceae; Populus.
-Web_seq: http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.download.ftp.html
-Web_db: http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html
+Web_seq: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v5.0/Ptrichocarpa/assembly/ 
+Web_db: http://www.phytozome.net/poplar.php
 Trna_opt: -o# -f# -m# -F# -Hy 
-Trna_abr: popTri1-tRNAs
-Gen_seq: /projects/lowelab/db/genomes/Euk/popTri1/popTri1-genome.fa
+Trna_abr: popTri2-tRNAs
+Gen_seq: /projects/lowelab/db/genomes/Euk/popTri2/popTri2-genome.fa
 
 Org_abr: Pfalc 
 Org_name: Plasmodium falciparum (Oct 2007)
 Domain:  Eukaryota
 Tax_ID:  36329: Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodium; Plasmodium (Laverania).
 Seq_acc:  NC_004325 NC_000910 NC_000521 NC_004318 NC_004326 NC_004327 NC_004328 NC_004329 NC_004330 NC_004314 NC_004315 NC_004316 NC_004331 NC_004317 NC_002375
 Name_chg: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chrM 
 Web_seq: ftp://ftp.ncbi.nih.gov/genomes/Protozoa/Plasmodium_falciparum
 Web_db:  http://plasmodb.org/
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: Pfalc-tRNAs 
 Gen_seq: /projects/lowelab/db/genomes/Protozoa/Plasmodium_falciparum/Pfalc-genome.fa
 Prot_seq: /projects/lowelab/db/genomes/Protozoa/Plasmodium_falciparum/Pfalc-prot.fa
 Feat_seq: /projects/lowelab/db/genomes/Protozoa/Plasmodium_falciparum/Pfalc-feat.fa
 
 Org_abr: Lmajo
 Org_name: Leishmania major (Version 5.0)
 Domain: Eukaryota
 Tax_ID: 347515: Eukaryota; Euglenozoa; Kinetoplastida; Trypanosomatidae; Leishmania; Leishmania; Leishmania major species complex; Leishmania major.
 Web_seq: ftp://ftp.sanger.ac.uk/pub/databases/L.major_sequences
 Web_db: http://www.genedb.org/genedb/leish/
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: Lmajo-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/leiMaj0/leiMaj0-genome.fa
 
 Org_abr: Osati
 Org_name: Oryza sativa
 Domain:  Eukaryota
 Tax_ID:  39947: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
 Seq_acc:  NC_008394 NC_008395 NC_008396 NC_008397 NC_008398 NC_008399 NC_008400 NC_008401 NC_008402 NC_008403 NC_008404 NC_008405
 Name_chg: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12
 Web_seq: ftp://ncbi.nlm.nih.gov/genomes/Oryza_sativa/
 Web_db:  http://www.tigr.org/tdb/e2k1/osa1/
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: Osati-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Oryza_sativa/Osati-genome.fa
 Prot_seq: /projects/lowelab/db/genomes/Oryza_sativa/Osati-prot.fa
 Feat_seq: /projects/lowelab/db/genomes/Oryza_sativa/Osati-feat.fa
 
 Org_abr: Sbico
 Org_name: Sorghum bicolor (Version 1.0)
 Domain: Eukaryota
 Tax_ID: 4558: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Liliopsida; commelinids; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Sorghum.
 Web_seq: http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html
 Web_db: http://genome.jgi-psf.org/Sorbi1/Sorbi1.home.html
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: Sbico-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/sorBic1/sorBic1-genome.fa
 
 Org_abr: Zmays
 Org_name: Zea mays (Version 3a.50)
 Domain: Eukaryota
 Tax_ID: 381124: Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Liliopsida; commelinids; Poales; Poaceae; PACCAD clade; Panicoideae; Andropogoneae; Zea; Zea mays.
 Web_seq: http://ftp.maizesequence.org/
 Web_db: http://www.maizesequence.org/index.html
 Trna_opt: -o# -f# -m# -F# -Hy
 Trna_abr: Zmays-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Euk/zeaMay3/zeaMay3-genome.fa
 
 Org_abr: Agamb
 Org_name: Anopheles gambiae
 Domain:  Eukaryota
 Tax_ID:  377270: Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Nematocera; Culicoidea; Culicidae; Anophelinae; Anopheles.
 Web_seq: ftp://ncbi.nlm.nih.gov/genomes/Anopheles_gambiae/
 Web_db:  http://genome.wustl.edu/genome.cgi?GENOME=Anopheles%20gambiae%20M
 Trna_opt: -o# -f# -m# -F# -Hy 
 Trna_abr: Agamb-tRNAs
 Gen_seq: /projects/lowelab/db/genomes/Anopheles_gambiae/Agamb-genome.fa
 

