src/hg/archaeStuff/data/Genome-info-meta 1.4
1.4 2009/05/27 17:23:34 pchan
add YNP sites 3, 4, 19
Index: src/hg/archaeStuff/data/Genome-info-meta
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-meta,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/archaeStuff/data/Genome-info-meta 3 May 2009 04:38:21 -0000 1.3
+++ src/hg/archaeStuff/data/Genome-info-meta 27 May 2009 17:23:34 -0000 1.4
@@ -1,74 +1,158 @@
## Genome-info-meta - only add fields for metagenomes 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;
# 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in correct place for unpublished genomes) using notation '&Org_abbr' i.e. (Dom_ct: &Heli_pylo_J99)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 brows
er)
# 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: Jose_coat_042308
Org_name: Josephs Coat 042308 assemblies
Menu_name: Josephs Coat (ystone1)
Iso_pub:
Domain: Archaea
DB_name: joseCoat_042308
DB_src: METAGENOME
Tax_name: Josephs coat YNP Site 1
BLAT_IDs: 61500 61501
Tax_ID: 183924: Archaea; Crenarchaeota; Thermoprotei.
TIGR_ID: 0
Dom_ct: 3001
Gen_ID: 0
Seq_acc: ystone1_JCVI_assemblies_042308 assembly
Name_chg: assembly
Gb_acc: None
Seq_size: 6730602
Seq_GC: 54.05
Gene_ct: 0
Multiz: PbacTtxCmaJcoTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),joseCoat_042308),therPend1)
Pub_id:
Rel_date: 04/23/08
Seq_src: Montana State University
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Jose_coat_042308-tRNAs
+
+Org_abr: Mona_geys_052609
+Org_name: Monarch Geyser 052609 Celera assembly
+Menu_name: Monarch Geyser 052609 (Site 3)
+Iso_pub:
+Domain: Archaea
+DB_name: monaGeys_052609
+DB_src: METAGENOME
+Tax_name: Monarch Geyser YNP Site 3
+BLAT_IDs: 61502 61503
+Tax_ID: 183924: Archaea; Crenarchaeota; Thermoprotei.
+TIGR_ID: 0
+Dom_ct: 3002
+Gen_ID: 0
+Seq_acc: ystone03.Celera.assemb.deg.singleton assembly
+Name_chg: assembly
+Gb_acc: None
+Seq_size: 18014660
+Seq_GC: 51.42
+Gene_ct: 1
+Multiz: PbacTtxCmaYNPTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Public_multiz: PbacCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Phylo: (((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),monaGeys_052609),joseCoat_052609),cistSpri_052609),therPend1)
+Pub_id:
+Rel_date: 05/26/09
+Seq_src: Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Mona_geys_052609-tRNAs
+
+Org_abr: Jose_coat_052609
+Org_name: Josephs Coat 052609 Celera assembly
+Menu_name: Josephs Coat 052609 (Site 4)
+Iso_pub:
+Domain: Archaea
+DB_name: joseCoat_052609
+DB_src: METAGENOME
+Tax_name: Josephs Coat YNP Site 4
+BLAT_IDs: 61504 61505
+Tax_ID: 183924: Archaea; Crenarchaeota; Thermoprotei.
+TIGR_ID: 0
+Dom_ct: 3003
+Gen_ID: 2
+Seq_acc: ystone04.Celera.assemb.deg.singleton assembly
+Name_chg: assembly
+Gb_acc: None
+Seq_size: 14766232
+Seq_GC: 52.32
+Gene_ct: 1
+Multiz: PbacTtxCmaYNPTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Public_multiz: PbacCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Phylo: ((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),monaGeys_052609),joseCoat_052609),joseCoat_042308),cistSpri_052609),therPend1)
+Pub_id:
+Rel_date: 05/26/09
+Seq_src: Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Jose_coat_052609-tRNAs
+
+Org_abr: Cist_spri_052609
+Org_name: Cistern Spring 052609 Celera assembly
+Menu_name: Cistern Spring 052609 (Site 5)
+Iso_pub:
+Domain: Archaea
+DB_name: cistSpri_052609
+DB_src: METAGENOME
+Tax_name: Cistern Spring YNP Site 19
+BLAT_IDs: 61506 61507
+Tax_ID: 183924: Archaea; Crenarchaeota; Thermoprotei.
+TIGR_ID: 0
+Dom_ct: 3004
+Gen_ID: 3
+Seq_acc: ystone19.Celera.assemb.deg.singleton assembly
+Name_chg: assembly
+Gb_acc: None
+Seq_size: 13987463
+Seq_GC: 50.27
+Gene_ct: 1
+Multiz: PbacTtxCmaYNPTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Public_multiz: PbacCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Phylo: (((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),monaGeys_052609),joseCoat_052609),cistSpri_052609),therPend1)
+Pub_id:
+Rel_date: 05/26/09
+Seq_src: Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Cist_spri_052609-tRNAs