Index: src/hg/archaeStuff/data/Genome-info-meta
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-meta,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/archaeStuff/data/Genome-info-meta	8 Jun 2009 20:15:45 -0000	1.8
+++ src/hg/archaeStuff/data/Genome-info-meta	20 Sep 2009 23:08:36 -0000	1.9
@@ -25,8 +25,10 @@
 # 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_name: Full name for each genome sequence in pairs (i.e. Chromosome1 chr1 Chromosome2 chr2 ..etc)
+# Related_org: Related organism names
 # 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
@@ -48,19 +50,21 @@
 Org_abr:  Jose_coat_042308
 Org_name: Josephs Coat 042308 assemblies
 Menu_name: Josephs Coat (ystone1)
 Iso_pub:
-Domain:   Archaea
+Domain:   Metagenome
 DB_name:  joseCoat_042308
 DB_src: METAGENOME
 Tax_name: Josephs coat YNP Site 1
 BLAT_IDs: 61500 61501
-Tax_ID:   183924: Archaea; Crenarchaeota; Thermoprotei.
+Tax_ID:   999999: Metagenome.
 TIGR_ID:  0
 Dom_ct: 3001
 Gen_ID:  0
 Seq_acc: ystone1_JCVI_assemblies_042308 assembly
 Name_chg: assembly
+Seq_name: assembly
+Related_org: Desulfurococcales Thermoproteales
 Gb_acc:   None
 Seq_size:  6730602
 Seq_GC:  54.05
 Gene_ct:  0 
@@ -73,22 +77,24 @@
 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)
+Org_name: Monarch Geyser 050609 JCVI Celera assembly
+Menu_name: Monarch Geyser 050609 (Site 3)
 Iso_pub:
-Domain:   Archaea
+Domain:   Metagenome
 DB_name:  monaGeys_052609
 DB_src: METAGENOME
 Tax_name: Monarch Geyser YNP Site 3
 BLAT_IDs: 61502 61503
-Tax_ID:   183924: Archaea; Crenarchaeota; Thermoprotei.
+Tax_ID:   999999: Metagenome.
 TIGR_ID:  0
 Dom_ct: 3002
 Gen_ID:  0
 Seq_acc: ystone03.Celera.assemb.deg.singleton assembly
 Name_chg: assembly
+Seq_name: assembly
+Related_org: Desulfurococcales Thermoproteales
 Gb_acc:   None
 Seq_size:  18014660
 Seq_GC:  51.42
 Gene_ct:  1 
@@ -101,22 +107,24 @@
 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)
+Org_name: Josephs Coat 050609 JCVI Celera assembly
+Menu_name: Josephs Coat 050609 (Site 4)
 Iso_pub:
-Domain:   Archaea
+Domain:   Metagenome
 DB_name:  joseCoat_052609
 DB_src: METAGENOME
 Tax_name: Josephs Coat YNP Site 4
 BLAT_IDs: 61504 61505
-Tax_ID:   183924: Archaea; Crenarchaeota; Thermoprotei.
+Tax_ID:   999999: Metagenome.
 TIGR_ID:  0
 Dom_ct: 3003
 Gen_ID:  2
 Seq_acc: ystone04.Celera.assemb.deg.singleton assembly
 Name_chg: assembly
+Seq_name: assembly
+Related_org: Desulfurococcales Thermoproteales
 Gb_acc:   None
 Seq_size:  14766232
 Seq_GC:  52.32
 Gene_ct:  1 
@@ -129,22 +137,24 @@
 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 19)
+Org_name: Cistern Spring 050609 JCVI Celera assembly
+Menu_name: Cistern Spring 050609 (Site 19)
 Iso_pub:
-Domain:   Archaea
+Domain:   Metagenome
 DB_name:  cistSpri_052609
 DB_src: METAGENOME
 Tax_name: Cistern Spring YNP Site 19
 BLAT_IDs: 61506 61507
-Tax_ID:   183924: Archaea; Crenarchaeota; Thermoprotei.
+Tax_ID:   999999: Metagenome.
 TIGR_ID:  0
 Dom_ct: 3004
 Gen_ID:  3
 Seq_acc: ystone19.Celera.assemb.deg.singleton assembly
 Name_chg: assembly
+Seq_name: assembly
+Related_org: Desulfurococcales Sulfolobales Thermoproteales
 Gb_acc:   None
 Seq_size:  13987463
 Seq_GC:  50.27
 Gene_ct:  1 
@@ -155,4 +165,184 @@
 Rel_date: 05/26/09
 Seq_src:  Montana State University
 Trna_opt: -o# -f# -m# -F# -HyA
 Trna_abr: Cist_spri_052609-tRNAs
+
+Org_abr:  Mona_geys_050609_2
+Org_name: Monarch Geyser 050609 JCVI Celera assembly
+Menu_name: Monarch Geyser 050609 (Site 3)
+Iso_pub:
+Domain:   Metagenome
+DB_name:  monaGeys_050609_2
+DB_src: METAGENOME
+Tax_name: Monarch Geyser YNP Site 3
+BLAT_IDs: 61508 61509
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3005
+Gen_ID:  4
+Seq_acc: Site_3_* DesulfI ThermoI ThermoII ThermoIII
+Name_chg: DesulfI ThermoI ThermoII ThermoIII
+Seq_name: Desulfurococcales_TypeI Thermoproteales_TypeI Thermoproteales_TypeII Thermoproteales_TypeIII
+Related_org: Desulfurococcales Thermoproteales
+Gb_acc:   None
+Seq_size:  1711839 3046415 316230 193173
+Seq_GC:  57 47 46 46
+Gene_ct:  1 
+Multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Public_multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Phylo:    ((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),nanEqu1),monaGeys_050609_2)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Mona_geys_050609-tRNAs
+
+Org_abr:  Jose_coat_050609_2
+Org_name: Josephs Coat 050609 JCVI Celera assembly
+Menu_name: Josephs Coat 050609 (Site 4)
+Iso_pub:
+Domain:   Metagenome
+DB_name:  joseCoat_050609_2
+DB_src: METAGENOME
+Tax_name: Josephs Coat YNP Site 4
+BLAT_IDs: 61510 61511
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3006
+Gen_ID:  5
+Seq_acc: Site_4_* DesulfI ThermoI ThermoII
+Name_chg: DesulfI ThermoI ThermoII
+Seq_name: Desulfurococcales_TypeI Thermoproteales_TypeI Thermoproteales_TypeII
+Related_org: Desulfurococcales Thermoproteales
+Gb_acc:   None
+Seq_size:  1541755 3908994 3138621
+Seq_GC:  56 48 59
+Gene_ct:  1 
+Multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1 joseCoat_042308
+Public_multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1 joseCoat_042308
+Phylo:    (((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),nanEqu1),joseCoat_050609_2),joseCoat_042308)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Jose_coat_050609-tRNAs
+
+Org_abr:  OSP_spri8_050609_1
+Org_name: OSP Spring 8 050609 JCVI Celera assembly
+Menu_name: OSP Spring 8 050609 (Site 8)
+Iso_pub:
+Domain:   Metagenome
+DB_name:  ospSpri8_050609_1
+DB_src: METAGENOME
+Tax_name: OSP Spring 8 YNP Site 8
+BLAT_IDs: 61512 61513
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3007
+Gen_ID:  6
+Seq_acc: Site_8_* CrenI DesulfI Myell Nano ThermoI
+Name_chg: CrenI DesulfI Myell Nano ThermoI
+Seq_name: Crenarchaeota_TypeI Desulfurococcales_TypeI M_yellowstonii Nanoarchaeum Thermoproteales_TypeI
+Related_org: Desulfurococcales Thermoproteales Metallosphaera Nanoarchaeum
+Gb_acc:   None
+Seq_size:  2042424 1436287 1156330 99725 2066274
+Seq_GC:  37 59 48 27 47
+Gene_ct:  1 
+Multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Public_multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Phylo:    ((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),nanEqu1),ospSpri8_050609_1)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: OSP_spri8_050609-tRNAs
+
+Org_abr:  OSP_spri14_050609_1
+Org_name: OSP Spring 14 050609 JCVI Celera assembly
+Menu_name: OSP Spring 14 050609 (Site 14)
+Iso_pub:
+Domain:   Metagenome
+DB_name:  ospSpri14_050609_1
+DB_src: METAGENOME
+Tax_name: OSP Spring 14 YNP Site 14
+BLAT_IDs: 61514 61515
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3008
+Gen_ID:  7
+Seq_acc: Site_14_* Hydro Myell Nano SulfoI ThermoI
+Name_chg: Hydro Myell Nano SulfoI ThermoI
+Seq_name: Hydrogenobaculum M_yellowstonii Nanoarchaeum Sulfolobales_TypeI Thermoproteales_TypeI
+Related_org: Hydrogenobaculum Thermoproteales Metallosphaera Sulfolobales Nanoarchaeum
+Gb_acc:   None
+Seq_size:  2042424 1436287 1156330 99725 2066274
+Seq_GC:  37 59 48 27 47
+Gene_ct:  1 
+Multiz:   ThermophilicYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 sulfIsla_Y_G_57_14 nanEqu1 hydrY04A
+Public_multiz:   ThermophilicYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 sulfIsla_Y_G_57_14 nanEqu1 hydrY04A
+Phylo:    ((((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),sulfIsla_Y_G_57_14),nanEqu1),hydrY04A),ospSpri14_050609_1)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: OSP_spri14_050609-tRNAs
+
+Org_abr:  Cist_spri_050609_2
+Org_name: Cistern Spring 050609 JCVI Celera assembly
+Menu_name: Cistern Spring 050609 (Site 19)
+Iso_pub:
+Domain:   Metagenome
+DB_name:  cistSpri_050609_2
+DB_src: METAGENOME
+Tax_name: Cistern Spring YNP Site 19
+BLAT_IDs: 61516 61517
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3009
+Gen_ID:  8
+Seq_acc: Site_19_* DesulfI SulfoI SulfoII ThermoI ThermoII
+Name_chg: DesulfI SulfoI SulfoII ThermoI ThermoII
+Seq_name: Desulfurococcales_TypeI Sulfolobales_TypeI Sulfolobales_TypeII Thermoproteales_TypeI Thermoproteales_TypeII
+Related_org: Desulfurococcales Thermoproteales Sulfolobales
+Gb_acc:   None
+Seq_size:  1523776 1770629 484936 3218059 1791250
+Seq_GC:  58 39 51 47 61
+Gene_ct:  1 
+Multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 sulfIsla_Y_G_57_14 nanEqu1
+Public_multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 sulfIsla_Y_G_57_14 nanEqu1
+Phylo:    (((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),sulfIsla_Y_G_57_14),nanEqu1),cistSpri_050609_2)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Cist_spri_050609-tRNAs
+
+Org_abr:  Beow_spri_East_D_072007_1
+Org_name: Beowulf Spring 050609 JCVI Celera assembly
+Menu_name: Beowulf Spring East Transect Point D 072007 
+Iso_pub:
+Domain:   Metagenome
+DB_name:  beowSpri_East_D_072007_1
+DB_src: METAGENOME
+Tax_name: Beowulf Spring East Transect Point D
+BLAT_IDs: 61518 61519
+Tax_ID:   999999: Metagenome.
+TIGR_ID:  0
+Dom_ct: 3010
+Gen_ID:  9
+Seq_acc: BED_* Staphy Thauma
+Name_chg: Staphy Thauma
+Seq_name: Staphylothermus Thaumarchaeota
+Related_org: Staphylothermus Thaumarchaeota
+Gb_acc:   None
+Seq_size:  1532059 1778986
+Seq_GC:  46 50
+Gene_ct:  1 
+Multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Public_multiz:   CrenNanoYNP pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1 igniHosp1 aerPer1 hypeButy1 desuKamc1 stapMari1 sulfAcid1 sulfToko1 sulSol1 nanEqu1
+Phylo:    ((((((((((((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1),igniHosp1),aerPer1),hypeButy1),desuKamc1),stapMari1),sulfAcid1),sulfToko1),sulSol1),nanEqu1),beowSpri_East_D_072007_1)
+Pub_id:   
+Rel_date: 09/14/09
+Seq_src:  Montana State University
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Beow_spri_072007-tRNAs

