src/hg/archaeStuff/data/Genome-info-mods 1.66
1.66 2009/05/03 04:38:21 pchan
add natrMaga0; fix multiz for vulcDist0 and joseCoat_042308
Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.65
retrieving revision 1.66
diff -b -B -U 4 -r1.65 -r1.66
--- src/hg/archaeStuff/data/Genome-info-mods 1 Apr 2009 12:13:45 -0000 1.65
+++ src/hg/archaeStuff/data/Genome-info-mods 3 May 2009 04:38:21 -0000 1.66
@@ -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 caldMaqu1 therPend1
-Public_multiz: PbacCmaTpe pyroArse1 pyroCali1 pyroIsla1 therNeut1 caldMaqu1 therPend1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacCmaTtxTpe 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)
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
@@ -574,11 +574,11 @@
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 caldMaqu1 therPend1
-Public_multiz: PbacCmaTpe therNeut1 pyrAer1 pyroArse1 pyroCali1 caldMaqu1 therPend1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacTtxCmaTpe therNeut1 pyrAer1 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)
Pub_id:
Rel_date: 12/20/06
Seq_src: DOE Joint Genome Institute/UCSC
Trna_opt: -o# -f# -m# -F# -HyA
@@ -593,22 +593,22 @@
DB_name: pyroCali1
Tax_name: Pyrobaculum calidifontis JCM 11548
TIGR_ID: 0
SP_ID: PYRAE
-Multiz: PbacTtxCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 therTena1 caldMaqu1 therPend1
-Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 caldMaqu1 therPend1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacTtxCmaTpe pyrAer1 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)
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 caldMaqu1 therPend1
-Public_multiz: PbacCmaTpe pyrAer1 pyroIsla1 therNeut1 pyroCali1 caldMaqu1 therPend1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacTtxCmaTpe 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)
Rel_date: April 2006
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_arse-tRNAs
SP_ID: PYRAE
@@ -622,35 +622,34 @@
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 caldMaqu1
-Public_multiz: PbacCmaTpe pyroIsla1 pyrAer1 pyroArse1 pyroCali1 caldMaqu1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacTtxCmaTpe pyroIsla1 pyrAer1 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)
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
-Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 pyroCali1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+Multiz: PbacTtxCmaTpe pyrAer1 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)
Rel_date: Nov 2007
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Cald_maqu-tRNAs
-Prot_seq: /projects/lowelab/db/genomes/Other-genomes/Caldivirga_maquilingensis/Cmaq-genome-prot.fa
Org_abr: Ther_pend_Hrk_5
DB_name: therPend1
Menu_name: Thermofilum pendens
-Iso_pub:
+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 pyroCali1 pyrAer1 pyroArse1 pyroIsla1 therNeut1
-Public_multiz: PbacCmaTpe caldMaqu1 pyroCali1 pyrAer1 pyroArse1 pyroIsla1 therNeut1
-Phylo: ((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),caldMaqu1),therPend1)
+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)
Rel_date: 03/01/06
Seq_src: DOE Joint Genome Institute
Trna_abr: Ther_pend-tRNAs
@@ -717,9 +716,9 @@
Seq_GC: 55.13
Gene_ct: 1800
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)
+Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: Private
Seq_src: University Duisburg-Essen
Trna_opt: -o# -f# -m# -F# -HyA
@@ -743,17 +742,42 @@
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 vulcDist0 caldMaqu1 therPend1
+Multiz: PbacTtxVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 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,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 03/2009
Seq_src: JGI
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Vulc_dist-tRNAs
+Org_name: Natrialba_magadii
+Menu_name: Natrialba_magadii
+Iso_pub: 9226918
+Domain: Archaea
+DB_name: natrMaga0
+DB_src: ORNL
+Tax_name: Natrialba magadii ATCC 43099
+BLAT_IDs: 61008 61009
+Tax_ID: 547559: Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Natrialba.
+TIGR_ID: 0
+Dom_ct: &Meth_hung_JF-1
+Gen_ID: 0
+Seq_acc: Nmag-assembly-04-2009 Contig73 Contig74 Contig75 Contig1 Contig2 Contig3 Contig4 Contig5 Contig6 Contig7 Contig8 Contig9 Contig10 Contig11 Contig12 Contig13 Contig14 Contig15 Contig16 Contig17 Contig18 Contig19 Contig20 Contig21 Contig22 Contig23 Contig24 Contig25 Contig26 Contig27 Contig28 Contig29 Contig30 Contig31 Contig32 Contig33 Contig34 Contig35 Contig36 Contig37 Contig38 Contig39 Contig40 Contig41 Contig42 Contig43 Contig44 Contig45 Contig46 Contig47 Contig48 Contig49 Contig50 Contig51 Contig52 Contig53 Contig54 Contig55 Contig56 Contig57 Contig58 Contig59 Contig60 Contig61 Contig62 Contig63 Contig64 Contig65 Contig66 Contig67 Contig68 Contig69 Contig70 Contig71 Contig72
+Name_chg: Contig73 Contig74 Contig75 Contig1 Contig2 Contig3 Contig4 Contig5 Contig6 Contig7 Contig8 Contig9 Contig10 Contig11 Contig12 Contig13 Contig14 Contig15 Contig16 Contig17 Contig18 Contig19 Contig20 Contig21 Contig22 Contig23 Contig24 Contig25 Contig26 Contig27 Contig28 Contig29 Contig30 Contig31 Contig32 Contig33 Contig34 Contig35 Contig36 Contig37 Contig38 Contig39 Contig40 Contig41 Contig42 Contig43 Contig44 Contig45 Contig46 Contig47 Contig48 Contig49 Contig50 Contig51 Contig52 Contig53 Contig54 Contig55 Contig56 Contig57 Contig58 Contig59 Contig60 Contig61 Contig62 Contig63 Contig64 Contig65 Contig66 Contig67 Contig68 Contig69 Contig70 Contig71 Contig72
+Seq_size: 58508 254969 4128710 983 869 1014 924 921 989 977 924 952 927 1398 1347 1265 935 1002 932 985 929 880 976 924 914 958 942 620 1013 865 961 554 997 938 900 905 947 976 611 766 965 759 969 924 920 985 865 951 938 925 960 893 922 854 997 935 1072 708 1288 1548 1514 1712 1239 1715 1400 1777 1675 1644 1935 1467 1992 2000 1381 1075 2013
+Seq_GC: 61.91 56.82 61.3 61.44 60.53 64.2 61.58 58.52 41.35 62.74 61.47 63.13 60.73 61.3 58.28 63.64 59.68 57.58 53.97 65.58 61.79 58.18 56.45 61.26 62.47 58.98 60.51 55.48 54.89 62.89 55.98 65.52 59.68 61.3 64.11 60.55 67.05 48.77 68.41 65.4 56.48 60.34 57.79 59.96 54.24 60.51 59.88 62.04 61.62 64.22 60.73 63.38 56.4 54.68 61.08 62.99 63.15 61.44 62.66 61.5 64.66 73.89 61.99 59.48 59.21 61.11 62.69 61.74 61.65 64.21 61.14 54.75 60.32 63.07 63.54
+Gene_ct: 0
+Pub_id:
+Rel_date: Private
+Seq_src: Joint Genome Institute
+Trna_opt: -o# -f# -m# -F# -HyA
+Trna_abr: Natr_maga-tRNAs
+Multiz: Halophiles haloWals1 natrPhar1 haloHalo1 haloSali1 halMar1
+Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+
Org_abr: Carb_hydr_Z-2901
Org_name: Carboxydothermus hydrogenoformans Z-2901
Menu_name: Carboxydothermus hydrogenoformans
Domain: Bacteria
@@ -903,9 +927,9 @@
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Stap_mari_F1
DB_name: stapMari1
-Iso_pub:
+Iso_pub: Fiala G, Stetter KO, Jannasch HW, Langworthy TA, and Madon J (1986) "<I>Staphylothermus marinus sp.</I> nov. represents a novel genus of extremely thermophilic submarine heterotrophic archaebacteria growing up to 98 degree C" (1986) <I>Systematic and Applied Microbiology</I> <B>8</B>: 106.
Multiz: Desulfurococcales desuKamc1 hypeButy1 aerPer1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Hype_buty
@@ -927,8 +951,10 @@
Org_abr: Desu_kamc_1221n
Menu_name: Desulfurococcus kamchatkensis
DB_name: desuKamc1
SP_ID: STAMF HYPBU AERPE
+Pub_id: 19114480
+Iso_pub:
Rel_date: Dec 2008
Seq_src: Institute of Microbiology of the Russian Academy of Sciences
Multiz: Desulfurococcales stapMari1 hypeButy1 aerPer1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)