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Tutorial
Jaci Saunders edited this page Jun 5, 2020
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- Download the backup database file for the pre-built database the working directory: Database File.
- Picking up after step 3 from the Installation Instructions, rebuild this database into the "metatryp2_proteins" empty database you just created.
sudo -u postgres pg_restore --dbname=metatryp2_proteins ./metatryp2_db_prot.backup
- Test that the database was successfully built by listing all the taxa in the Genomes data category. (Schema to support the data categories Specialized Assemblies and Meta-omic Assemblies is also loaded into
metatryp2_proteins
; however, there is no pre-loaded sequence or taxonomic data for these data types.
./bin/list_taxons.sh
- Can now query these genomes, or add to this database by following instructions in Quick Usage Guide.
- Full taxonomic lineages can be found here.
- Taxa listed below:
- Aciduliprofundum boonei T469
- Alcanivorax sp. DG881
- Algoriphagus machipongonensis PR1
- Alphaproteobacteria sp. SAR11 HIMB5
- Alteromonas australica H17
- Alteromonas macleodii Black Sea 11
- Alteromonas macleodii D7
- Alteromonas macleodii DE
- Alteromonas macleodii HOT1A3
- Alteromonas macleodii MIT1002
- Alteromonas macleodii REDSEA-S09_B2
- Alteromonas macleodii REDSEA-S12_B5
- Alteromonas macleodii REDSEA-S15_B11
- Alteromonas mediterranea DE
- Alteromonas sp. ALT199
- Bacillus sp. B14905
- Bacillus sp. NRRL B-14911
- Bacillus sp. SG-1
- Beggiatoa sp. Orange Guaymas
- Brevundimonas sp. BAL3
- Caminibacter mediatlanticus TB-2
- Candidatus Nitrosopelagicus brevis CN25
- Candidatus Pelagibacter ubique SAR11 HTCC1062
- Carnobacterium sp. AT7
- Citreicella sp. SE45
- Congregibacter litoralis KT71
- Crocosphaera watsonii WH 0003
- Crocosphaera watsonii WH 0005
- Crocosphaera watsonii WH 0401 (draft1)
- Crocosphaera watsonii WH 0402
- Crocosphaera watsonii WH 8501
- Crocosphaera watsonii WH 8502
- Cyanobium sp. PCC 7001
- Erythrobacter litoralis HTCC2594
- Erythrobacter sp. NAP1
- Erythrobacter sp. SD-21
- Flavobacteria bacterium BAL38
- Flavobacteria bacterium BBFL7
- Fulvimarina pelagi HTCC2506
- Gammaproteobacteria sp. OM60 HIMB55
- Hydrogenivirga sp. 128-5-R1-1
- Idiomarina baltica OS145
- Janibacter sp. HTCC2649
- Kordia algicida OT-1
- Lentisphaera araneosa HTCC2155
- Limnobacter sp. MED105
- Loktanella sp. SE62
- Loktanella vestfoldensis SKA53
- marine actinobacterium PHSC20C1
- Marinitoga piezophila KA3
- Microbulbifer agarilyticus S89
- Nitrobacter hamburgensis X14
- Nitrococcus mobilis Nb-231
- Nitrosopelagicus brevis 1
- Nitrosopelagicus sp. REDSEA-S32_B2
- Nitrosopumilus maritimus SCM1
- Nitrospina sp. AB-629-B18
- Nitrospina sp. SCGC AAA799-A02
- Nitrospina sp. SCGC AAA799-C22
- Nitrospira defluvii
- Planctomycetaceae bacterium KSU-1
- Prochlorococcus marinus MIT9312
- Prochlorococcus sp. MIT9201
- Prochlorococcus sp. MIT9202
- Prochlorococcus sp. MIT9211
- Prochlorococcus sp. MIT9215
- Prochlorococcus sp. MIT9301
- Prochlorococcus sp. MIT9302
- Prochlorococcus sp. MIT9303
- Prochlorococcus sp. MIT9311
- Prochlorococcus sp. MIT9314
- Prochlorococcus sp. MIT9321
- Prochlorococcus sp. MIT9322
- Prochlorococcus sp. MIT9401
- Prochlorococcus sp. MIT9515
- Prochlorococcus sp. NATL1A
- Prochlorococcus sp. NATL2A
- Prochlorococcus sp. SB
- Prochlorococcus sp. SS35
- Prochlorococcus sp. SS51
- Prochlorococcus sp. SS52
- Pseudoalteromonas arctica A 37-1-2
- Pseudoalteromonas atlantica T6c
- Pseudoalteromonas atlantica TB41
- Pseudoalteromonas denitrificans DSM 6059
- Pseudoalteromonas piscicida ATCC 15057
- Pseudoalteromonas rubra ATCC 29570
- Pseudoalteromonas rubra S2471
- Richelia intracellularis RC01
- Roseobacter litoralis Och 149
- Roseobacter sp. AzwK-3b
- Roseobacter sp. CCS2
- Roseobacter sp. GAI101
- Roseobacter sp. MED193
- Roseobacter sp. SK209-2-6
- Roseovarius nubinhibens ISM
- Roseovarius sp. TM1035
- Sagittula stellata E-37
- SAR116 cluster alpha proteobacterium sp. HIMB100
- SAR116 cluster alphaproteobacterium REDSEA-S10_B10N8
- SAR116 cluster alphaproteobacterium REDSEA-S2_B12
- Shewanella benthica KT99
- Sphingomonas sp. SKA58
- Stenotrophomonas sp. SKA14
- Sulfitobacter sp. EE-36
- Sulfitobacter sp. NAS-14.1
- Sulfurospirillum sp. Am-N (draft)
- Synechococcus elongatus PCC 6301
- Synechococcus elongatus PCC 7942
- Synechococcus sp. 7002
- Synechococcus sp. BL107
- Synechococcus sp. CB0101
- Synechococcus sp. CB0205
- Synechococcus sp. CC9311
- Synechococcus sp. CC9605
- Synechococcus sp. CC9616
- Synechococcus sp. CC9902
- Synechococcus sp. PCC 7336
- Synechococcus sp. RS9916
- Synechococcus sp. RS9917
- Synechococcus sp. WH 8016
- Synechococcus sp. WH 8109
- Synechococcus sp. WH5701
- Synechococcus sp. WH7803
- Synechococcus sp. WH7805
- Synechococcus sp. WH8102
- Thalassobium sp. R2A62
- Thermococcus sp. AM4
- Trichodesmium erythraeum IMS101
- Trichodesmium thiebautii H9-4
- Vibrio alginolyticus 12G01
- Vibrio campbellii AND4
- Vibrio fischeri MJ11
- Vibrio parahaemolyticus 16
- Vibrio sp. MED222
- Vibrio splendidus 12B01