src/hg/archaeStuff/data/Genome-info-meta 1.1

Index: src/hg/archaeStuff/data/Genome-info-meta
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RCS file: src/hg/archaeStuff/data/Genome-info-meta
diff -N src/hg/archaeStuff/data/Genome-info-meta
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/archaeStuff/data/Genome-info-meta	31 Mar 2009 06:58:10 -0000	1.1
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+## 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+           in correct place for unpublished genomes) using notation '&Org_abbr' i.e. (Dom_ct: &Heli_pylo_J99)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 042308 assemblies
+Iso_pub:
+Domain:   Archaea
+DB_name:  joseCoat_042308
+#Cent_DB:  centraldb_pbac
+DB_src: METAGENOME
+Tax_name: Josephs coat
+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:   PbacTtxCmaTpe 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),therPend1)
+Pub_id:   
+Rel_date: Private
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Jose_coat_042308-tRNAs