src/hg/archaeStuff/data/Genome-info-mods 1.83
1.83 2009/09/30 06:59:54 pchan
change methFerv0 to methFerv1; add public multiz for halos to exclude natrMaga0; add info for haloUtah1
Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.82
retrieving revision 1.83
diff -b -B -U 4 -r1.82 -r1.83
--- src/hg/archaeStuff/data/Genome-info-mods 29 Sep 2009 20:08:16 -0000 1.82
+++ src/hg/archaeStuff/data/Genome-info-mods 30 Sep 2009 06:59:54 -0000 1.83
@@ -81,17 +81,19 @@
DB_name: halMar1
Iso_pub: 11536469
Rel_date: Nov. 2004
Sp_info: <I>H. marismortui</I> is a halophilic archaeon found in the Dead Sea, where it optimally grows at around 4.5 molar salt.
-Multiz: Halophiles natrPhar1 haloWals1 haloVolc1 natrMaga0 haloHalo1 haloSali1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv natrPhar1 haloWals1 haloUtah1 haloVolc1 natrMaga0 haloHalo1 haloSali1
+Public_multiz: Halophiles natrPhar1 haloWals1 haloUtah1 haloVolc1 haloHalo1 haloSali1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Halo_sp
DB_name: haloHalo1
Rel_date: Oct 2000
Sp_info: <I>Halobacterium</I> is a halophilic aerobic euryarchaeon found under conditions of extremely high salinity, at an optimum of 4.3M salt. It is a mesophile which grows optimally at 42C. A well-developed genetic system is available for this species.
-Multiz: Halophiles haloSali1 natrMaga0 haloVolc1 natrPhar1 haloWals1 halMar1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv haloSali1 natrMaga0 haloVolc1 natrPhar1 haloWals1 halMar1 haloUtah1
+Public_multiz: Halophiles haloSali1 haloVolc1 natrPhar1 haloWals1 halMar1 haloUtah1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
SP_ID: HALSA
Org_abr: Halo_sali_R1
Menu_name: Halobacterium salinarum R1
@@ -99,20 +101,22 @@
Rel_date: Feb 2008
Seq_src: Max Planck Institute
SP_ID: HALSA
Iso_pub:
-Multiz: Halophiles haloHalo1 natrMaga0 haloVolc1 natrPhar1 haloWals1 halMar1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv haloHalo1 natrMaga0 haloVolc1 natrPhar1 haloWals1 halMar1 haloUtah1
+Public_multiz: Halophiles haloHalo1 haloVolc1 natrPhar1 haloWals1 halMar1 haloUtah1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Halo_wals
Rel_date: 07/25/06
Seq_src: Max-Planck-Institute of Biochemistry and the University of Groningen
Pub_id: 16820047
DB_name: haloWals1
#Iso_pub: 15560825
SP_ID: HALWD HALMA HALSP NATPD
-Multiz: Halophiles haloVolc1 halMar1 natrPhar1 natrMaga0 haloHalo1 haloSali1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv haloVolc1 halMar1 haloUtah1 natrPhar1 natrMaga0 haloHalo1 haloSali1
+Public_multiz: Halophiles haloVolc1 halMar1 haloUtah1 natrPhar1 haloHalo1 haloSali1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Halo_volc_DS2
Org_name: Haloferax volcanii DS2
Menu_name: Haloferax volcanii
@@ -133,10 +137,11 @@
Seq_size: 2847757 635786 437906 85092 6359
Seq_GC: 66.64 61.67 65.56 55.5 56.06
Gene_ct: 4209
Gb_acc: None
-Multiz: Halophiles haloWals1 natrPhar1 natrMaga0 haloHalo1 haloSali1 halMar1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv haloWals1 natrPhar1 natrMaga0 haloHalo1 haloSali1 halMar1 haloUtah1
+Public_multiz: Halophiles haloWals1 natrPhar1 haloHalo1 haloSali1 halMar1 haloUtah1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Pub_id:
Rel_date: April 2007
Seq_src: Institute for Genomic Research
Sp_info: The genome is complete and being publicly released by Jonathan Eisen before journal publication while genome annotation is in progress. <I>H. volcanii</I> is a chemoorganotroph requiring complex nutrient medium and 1.5-2.5 M NaCl for growth. Cultures will grow at 37C, but optimal growth is at 42C.
@@ -148,26 +153,32 @@
Org_abr: Halo_utah_DSM_12940
DB_name: haloUtah1
Name_chg: chr
+Iso_pub: 10826803
+Rel_date: April 2009
+Multiz: HalophilesPriv haloWals1 natrPhar1 natrMaga0 haloHalo1 haloSali1 halMar1
+Public_multiz: Halophiles haloWals1 natrPhar1 haloHalo1 haloSali1 halMar1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Natr_phar
DB_name: natrPhar1
Iso_pub:
Rel_date: Oct 2005
Sp_info: <I>N. pharaonis</I> grows at high salt and pH and has multiple systems for nitrogen assimilation.
-Multiz: Halophiles haloWals1 haloHalo1 natrMaga0 haloSali1 haloVolc1 halMar1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: HalophilesPriv haloWals1 haloHalo1 natrMaga0 haloSali1 haloVolc1 halMar1 haloUtah1
+Public_multiz: Halophiles haloWals1 haloHalo1 haloSali1 haloVolc1 halMar1 haloUtah1
+Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Meth_jann
DB_name: methJann1
Iso_pub: http://www.springerlink.com/content/u8774k126821777x/
Name_chg: chr lg_extrachr sm_extrachr
TIGR_ID: 57
Rel_date: August 1996
Sp_info: The organism's genus was formerly <I>Methanococcus</I>, but it has been reclassified as <I>Methanocaldococcus</I>. <I>M. jannaschii</I> is a methanogen which grows optimally at 85C, and has the distinction of being the first archaeon and first hyperthermophile sequenced.
-Multiz: Methanococcus methFerv0 methVulc0 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
-Phylo: (methKand1,(methTher1,(((methJann1,methFerv0),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
+Multiz: Methanococcus methFerv1 methVulc0 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
+Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_mari_S2
Menu_name: Methanococcus maripaludis S2
DB_name: metMar1
@@ -213,17 +224,17 @@
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Org_abr: Meth_ferv_AG86
Menu_name: Methanocaldococcus fervens
-DB_name: methFerv0
+DB_name: methFerv1
Iso_pub: 10319479
Tax_name: Methanocaldococcus fervens AG86
SP_ID: METJA
Rel_date: July 2009
-Name_chg: ctg00024 ctg00058 ctg00051 ctg00061 ctg00035 ctg00020 ctg00057 ctg00015 ctg00029 ctg00040 ctg00028 ctg00065 ctg00060 ctg00030 ctg00026 ctg00022 ctg00045 ctg00032 ctg00031 ctg00017 ctg00016 ctg00008 ctg00013 ctg00014 ctg00021 ctg00033 ctg00036 ctg00025 ctg00034 ctg00003 ctg00023 ctg00018 ctg00027 ctg00019
+Name_chg: chr pMEFER01
Seq_src: Joint Genome Institute
Multiz: Methanococcus methJann1 methVulc0 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
-Phylo: (methKand1,(methTher1,(((methJann1,methFerv0),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
+Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_infe_ME
Menu_name: Methanocaldococcus infernus
DB_name: methInfe0
@@ -232,10 +243,10 @@
SP_ID: METJA
Rel_date: July 2009
Name_chg: ctg00065 ctg00004 ctg00020 ctg00072 ctg00034 ctg00022 ctg00031 ctg00044 ctg00045 ctg00063 ctg00039 ctg00103 ctg00043 ctg00019 ctg00040 ctg00051 ctg00026 ctg00037 ctg00018 ctg00010 ctg00085 ctg00032 ctg00028 ctg00021 ctg00049 ctg00052 ctg00042 ctg00095 ctg00038 ctg00033 ctg00081 ctg00070 ctg00113 ctg00016 ctg00002 ctg00069 ctg00024 ctg00027 ctg00108 ctg00017 ctg00107 ctg00062 ctg00036 ctg00029 ctg00035 ctg00041 ctg00023 ctg00009 ctg00047 ctg00082 ctg00025 ctg00046 ctg00030 ctg00059
Seq_src: Joint Genome Institute
-Multiz: Methanococcus methJann1 methFerv0 methVulc0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
-Phylo: (methKand1,(methTher1,(((methJann1,methFerv0),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
+Multiz: Methanococcus methJann1 methFerv1 methVulc0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
+Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_vulc_M7
Org_name: Methanocaldococcus vulcanius M7
Menu_name: Methanocaldococcus vulcanius
@@ -255,10 +266,10 @@
Name_chg: Contig4 Contig6 Contig7 Contig2 Contig3 Contig5
Seq_size: 729534 713986 110152 104703 44189 38809
Seq_GC: 31.48 31.26 31.57 32.04 30.53 31.97
Seq_src: Joint Genome Institute
-Multiz: Methanococcus methJann1 methFerv0 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
-Phylo: (methKand1,(methTher1,(((methJann1,methFerv0),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
+Multiz: Methanococcus methJann1 methFerv1 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
+Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc0),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_acet
DB_name: metAce1
Rel_date: April 2002
@@ -897,9 +908,9 @@
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 pyroOgun03 pyroArse1 caldMaqu1 therPend1
-Public_multiz: PbacVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 vulcDist0 caldMaqu1 therPend1
+Public_multiz: PbacVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 03/2009
Seq_src: JGI
@@ -933,10 +944,10 @@
Rel_date: Private
Seq_src: Joint Genome Institute
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Natr_maga-tRNAs
-Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloWals1 haloVolc1
-Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),(haloWals1,haloVolc1))
+Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1
+Phylo: (((((haloHalo1,haloSali1),natrMaga0),natrPhar1),halMar1),haloUtah1),(haloWals1,haloVolc1))
Org_abr: Carb_hydr_Z-2901
Org_name: Carboxydothermus hydrogenoformans Z-2901
Menu_name: Carboxydothermus hydrogenoformans