src/hg/archaeStuff/data/Genome-info-mods 1.68
1.68 2009/07/15 02:47:08 lowe
Added two new Thermococcus genomes, still need multiz tracks
Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.67
retrieving revision 1.68
diff -b -B -U 4 -r1.67 -r1.68
--- src/hg/archaeStuff/data/Genome-info-mods 5 May 2009 20:44:11 -0000 1.67
+++ src/hg/archaeStuff/data/Genome-info-mods 15 Jul 2009 02:47:08 -0000 1.68
@@ -326,11 +326,11 @@
Org_abr: Pyro_aero
DB_name: pyrAer1
Iso_pub: 7692819
#Cent_DB: centraldb_pbac
-Multiz: PbacCmaTtxTpe pyroArse1 pyroCali1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacCmaTtxTpe pyroOgun0 pyroArse1 pyroCali1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroArse1 pyroCali1 pyroIsla1 therNeut1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: Dec 2001
Sp_info: <I>P. aerophilum</I> is a hyperthermophilic crenarchaeon which was isolated from a boiling marine hole at Martoni Beach, Italy. It grows optimally at 100 C, either in the presence of low amounts of oxygen or anaerobically. It is remarkable for being able to utilize five different oxidants in respiration: oxygen, nitrate, arsenate, selenate, iron (III), and thiosulfate. The genome was sequenced and annotated as the PhD project of Sorel Fitz-Gibbon, a student in Jeffrey Miller's lab.
Org_abr: Pyro_abys
@@ -390,8 +390,27 @@
Seq_src: Korea Ocean Research & Development Institute
Multiz: Thermococcales therKoda1 therBaro0 pyrFur2 pyrAby1 pyrHor1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+Org_abr: Ther_gamm_EJ3
+Menu_name: Thermococcus gammatolerans
+DB_name: therGamm1
+Seq_acc: NC_012804
+Name_chg: chr
+Pub_id: 0
+#Pub_id: 12807211
+Rel_date: June 2009
+SP_ID: PYRKO
+
+Org_abr: Ther_sibi_MM_739
+Menu_name: Thermococcus sibiricus
+DB_name: therSibi1
+SP_ID: PYRKO
+Seq_acc: NC_012883
+Name_chg: chr
+Pub_id: 11354459
+Rel_date: July 2009
+
Org_abr: Sulf_acid_DSM_639
Menu_name: Sulfolobus acidocaldarius
Iso_pub: 4559703
DB_name: sulfAcid1
@@ -574,11 +593,11 @@
Menu_name: Pyrobaculum islandicum
DB_name: pyroIsla1
Iso_pub: http://www.springerlink.com/content/j7016363n25h5221/
SP_ID: PYRAE
-Multiz: PbacTtxCmaTpe therNeut1 pyrAer1 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacTtxCmaTpe therNeut1 pyrAer1 pyroOgun0 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe therNeut1 pyrAer1 pyroArse1 pyroCali1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 12/20/06
Seq_src: DOE Joint Genome Institute/UCSC
Trna_opt: -o# -f# -m# -F# -HyA
@@ -593,22 +612,22 @@
DB_name: pyroCali1
Tax_name: Pyrobaculum calidifontis JCM 11548
TIGR_ID: 0
SP_ID: PYRAE
-Multiz: PbacTtxCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacTtxCmaTpe pyrAer1 pyroOgun0 pyroArse1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: 02/27/07
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_cali-tRNA
Org_abr: Pyro_arse_DSM_13514
Menu_name: Pyrobaculum arsenaticum
DB_name: pyroArse1
Iso_pub: 11108007
-Multiz: PbacTtxCmaTpe pyrAer1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacTtxCmaTpe pyroOgun0 pyrAer1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyrAer1 pyroIsla1 therNeut1 pyroCali1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: April 2006
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_arse-tRNAs
SP_ID: PYRAE
@@ -622,21 +641,51 @@
Iso_pub:
Rel_date: Mar 2008
Seq_src: DOE Joint Genome Institute / UCSC
Trna_abr: Ther_neut-tRNAs
-Multiz: PbacTtxCmaTpe pyroIsla1 pyrAer1 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacTtxCmaTpe pyroIsla1 pyrAer1 pyroOgun0 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroIsla1 pyrAer1 pyroArse1 pyroCali1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+
+Org_abr: Pyro_ogun
+Org_name: Pyrobaculum oguniense
+Menu_name: Pyrobaculum oguniense
+Domain: Archaea
+DB_name: pyroOgun0
+DB_src: LOWELAB
+Tax_name: Pyrobaculum oguniense
+Tax_ID: 99007: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum.
+Iso_pub: 11321074
+BLAT_IDs: 61015 61016
+TIGR_ID: 0
+JGI_ID: 0
+SP_ID: PYRAE
+String_ID: 0
+Dom_ct: &Pyro_isla_DSM_4184
+Gen_ID: 0
+Gb_acc: None
+Seq_acc: Pog-genome-v0 chr plasmid
+Name_chg: chr ece
+Seq_size: 2434148 16919
+Seq_GC: 55.08 50.45
+Gene_ct: 3206
+Multiz: PbacTtxCmaTpe pyroArse1 pyrAer1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
+Public_multiz: PbacCmaTpe pyroArse1 pyrAer1 pyroIsla1 therNeut1 pyroCali1 vulcDist0 caldMaqu1 therPend1
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Rel_date: 07/10/09
+Seq_src: UC Santa Cruz
+Trna_abr: Pyro_ogun-tRNAs
+
Org_abr: Cald_maqu_IC-167
Menu_name: Caldivirga maquilingensis
Domain: Archaea
Iso_pub: 10425774
DB_name: caldMaqu1
SP_ID: PYRAE
-Multiz: PbacTtxCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0
+Multiz: PbacTtxCmaTpe pyrAer1 pyroOgun0 pyroArse1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0
Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 pyroCali1 vulcDist0
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: Nov 2007
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Cald_maqu-tRNAs
@@ -646,10 +695,10 @@
Iso_pub: Zillig, W., A. Gierl, G. Schreiber, S. Wunderl, D. Janekovic, K. O. Stetter, and H. P. Klenk. (1983) "The archaebacterium <I>Thermofilum pendens</I> represents a novel genus of the thermophilic, anaerobic sulfur respiring Thermoproteales." <I>Syst. Appl. Microbiol.</I> <B>4</B>:79-87.
Seq_acc: NC_008696 NC_008698
Name_chg: pTPEN01 chr
Multiz: PbacTtxCmaTpe caldMaqu1 vulcDist0 pyroCali1 pyrAer1 pyroArse1 pyroIsla1 therNeut1
-Public_multiz: PbacCmaTpe caldMaqu1 vulcDist0 pyroCali1 pyrAer1 pyroArse1 pyroIsla1 therNeut1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Public_multiz: PbacCmaTpe caldMaqu1 vulcDist0 pyroCali1 pyrAer1 pyroOgun0 pyroArse1 pyroIsla1 therNeut1
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: 03/01/06
Seq_src: DOE Joint Genome Institute
Trna_abr: Ther_pend-tRNAs
@@ -706,9 +755,9 @@
Tax_name: Thermoproteus tenax
BLAT_IDs: 61004 61005
Tax_ID: 2271: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Thermoproteus.
TIGR_ID: 0
-Dom_ct: &Ther_neut
+Dom_ct: &Ther_neut_V24Sta
Gen_ID: 0
Seq_acc: Ttenax-genome chr
Name_chg: chr
Gb_acc: None
@@ -734,19 +783,19 @@
Tax_name: Vulcanisaeta distributa IC-017
BLAT_IDs: 61006 61007
Tax_ID: 572478: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Vulcanisaeta.
TIGR_ID: 0
-Dom_ct: &Ther_neut
+Dom_ct: &Ther_tena
Gen_ID: 0
Seq_acc: Vdistributa-genome Contig00003 Contig00014 Contig00022 Contig00023 Contig00024 Contig00025 Contig00026 Contig00027 Contig00028 Contig00029 Contig00030 Contig00031 Contig00032 Contig00033 Contig00034 Contig00035 Contig00036
Name_chg: Contig00003 Contig00014 Contig00022 Contig00023 Contig00024 Contig00025 Contig00026 Contig00027 Contig00028 Contig00029 Contig00030 Contig00031 Contig00032 Contig00033 Contig00034 Contig00035 Contig00036
Gb_acc: None
Seq_size: 534 515 264733 65541 174207 139013 122896 196801 158953 39744 100608 15899 178459 562434 78852 109394 157801
Seq_GC: 42.7 42.33 44.63 44.66 45.67 44.93 46.6 47.02 46.38 50.39 50.63 48.37 43.6 44.3 45.13 44.15 45.72
Gene_ct: 2634
-Multiz: PbacTtxVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
+Multiz: PbacTtxVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroOgun0 pyroArse1 caldMaqu1 therPend1
Public_multiz: PbacVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 vulcDist0 caldMaqu1 therPend1
-Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
+Phylo: ((((((((pyroArse1,pyroOgun0),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 03/2009
Seq_src: JGI
Trna_opt: -o# -f# -m# -F# -HyA