Genome Informatics Laboratory at KRIBB

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== Public genomes for comparison ======

향후 변동될 수 있으며 다음에 보인 KRIBB 등록 균주 중 일부(별표)는 표준 균주가 아니다(KRIBB에서 이미 등록한 genome을 포함하였음; 그러나 본 프로젝트와 관련이 없을 수도 있음). KRIBB 등록 균주가 아닌 것은 전부 표준 균주이다. 각 row는 <assembley accession> <name> <strain name>의 컬럼으로 이루어져 있다. Name은 예전에는 species + strain까지 다 포함하여 등록을 하는 경향이 있었지만 요즘은 species name으로 줄여서 등록하고 균주명은 별도로 등록하는 경향이 있다.

최종 정리일:  --- //[[hyjeong@kribb.re.kr|Haeyoung Jeong]] 2025/01/17 16:51//

    * GCA_000773685.1 Acinetobacter sp. HR7*
    * GCA_000773675.1 Bordetella trematum     HR18*
    * GCA_001650325.1 Exiguobacterium undae   KCTC 3810
    * GCA_001895205.1 Vibrio injensis M12-1144
    * GCA_004916975.1 Paenibacillus dokdonensis       YH-JAE5
    * GCA_001742425.1 Bacillus solimangrovi   GH2-4

  GCA_000773685.1	Acinetobacter sp. HR7	HR7*
  GCA_001552675.1	Alicyclobacillus sendaiensis NBRC 100866	NBRC 100866
  GCA_000829535.1	Bacillus badius	MTCC 1458
  GCA_001591605.1	Bacillus badius NBRC 15713	NBRC 15713
  GCA_001742425.1	Bacillus solimangrovi	GH2-4
  GCA_004340925.1	Blautia coccoides	DSM 935
  GCA_034355335.1	Blautia coccoides	DSM 935
  GCA_900461125.1	Blautia coccoides	NCTC11035
  GCA_900078335.1	Bordetella trematum	NCTC12995
  GCA_900445945.1	Bordetella trematum	NCTC12995
  GCA_000773675.1	Bordetella trematum	HR18*
  GCA_003710915.1	Brevibacillus invocatus	JCM 12215
  GCA_000525915.1	Brochothrix campestris FSL F6-1037	FSL F6-1037
  GCA_900445365.1	Cytobacillus firmus	NCTC10335
  GCA_001591465.1	Cytobacillus firmus NBRC 15306	NBRC 15306
  GCA_002835735.1	Cytobacillus horneckiae	1P01SC
  GCA_042649545.1	Cytobacillus kochii	CCUG 59877
  GCA_030812975.1	Cytobacillus kochii	DSM 23667
  GCA_001650325.1	Exiguobacterium undae	KCTC 3810
  GCA_000620805.1	Exiguobacterium undae DSM 14481	DSM 14481
  GCA_017872935.1	Formosa algae	DSM 15523
  GCA_001439665.1	Formosa algae	KMM 3553
  GCA_001678675.1	Gelidibacter algens	ACAM 536
  GCA_003259265.1	Gelidibacter algens	DSM 12408
  GCA_000025345.1	Geodermatophilus obscurus DSM 43160	DSM 43160
  GCA_039544795.1	Geodermatophilus obscurus DSM 43160	NBRC 13315
  GCA_020731255.1	Gordonia bronchialis	FDAARGOS_1594
  GCA_900450805.1	Gordonia bronchialis	NCTC10667
  GCA_000024785.1	Gordonia bronchialis DSM 43247	DSM 43247
  GCA_001420715.1	Heyndrickxia shackletonii	LMG 18435
  GCA_011008805.1	Heyndrickxia shackletonii	LMG 18435
  GCA_040801915.1	Jeotgalibacillus marinus	DSM 1297
  GCA_900478165.1	Lederbergia lenta	NCTC4824
  GCA_001591545.1	Lederbergia lenta NBRC 16444	NBRC 16444
  GCA_000708755.2	Metabacillus indicus LMG 22858	LMG 22858
  GCA_900103415.1	Methanobrevibacter millerae	DSM 16643
  GCA_900114585.1	Methanobrevibacter olleyae	DSM 16632
  GCA_000016525.1	Methanobrevibacter smithii ATCC 35061	ATCC 35061; PS; DSMZ 861
  GCA_028743435.1	Methanobrevibacter smithii ATCC 35061	DSM 861
  GCA_001591585.1	Niallia circulans NBRC 13626	NBRC 13626
  GCA_021532375.1	Paenibacillus alkaliterrae	DSM 17040
  GCA_004001025.1	Paenibacillus amylolyticus	NBRC 15957
  GCA_004117095.1	Paenibacillus chitinolyticus	KCCM 41400
  GCA_026797105.1	Paenibacillus chitinolyticus	NRRL B-23119
  GCA_000739915.1	Paenibacillus chitinolyticus NBRC 15660	NBRC 15660
  GCA_004916975.1	Paenibacillus dokdonensis	YH-JAE5
  GCA_001632305.1	Paenibacillus glucanolyticus	5162
  GCA_004000885.1	Paenibacillus glucanolyticus NBRC 15330	NBRC 15330
  GCA_004000805.1	Paenibacillus glycanilyticus NBRC 16618	NBRC 16618
  GCA_015473105.1	Paenibacillus glycanilyticus subsp. hiroshimensis	CCI5
  GCA_004000825.1	Paenibacillus kobensis NBRC 15729	NBRC 15729
  GCA_001514495.1	Paenibacillus pabuli NBRC 13638	NBRC 13638
  GCA_014192015.1	Paenibacillus rhizosphaerae	CECT 5831
  GCA_000758685.1	Paenibacillus stellifer	DSM 14472
  GCA_002161855.1	Paenibacillus thiaminolyticus	NRRL B-4156
  GCA_007066085.1	Paenibacillus thiaminolyticus	NRRL B-4156
  GCA_004001005.1	Paenibacillus thiaminolyticus NBRC 15656 = DSM 7262	NBRC 15656
  GCA_017873435.1	Paenibacillus turicensis	DSM 14349
  GCA_004000985.1	Paenibacillus validus NBRC 15382	NBRC 15382
  GCA_001687625.2	Planococcus maritimus	DSM 17275
  GCA_001591565.1	Priestia flexa NBRC 15715	NBRC 15715
  GCA_001274935.1	Priestia koreensis	DSM 16467
  GCA_002259605.1	Pseudoscardovia radai	DSM 24742
  GCA_900002825.1	Romboutsia lituseburensis	A25K
  GCA_900103615.1	Romboutsia lituseburensis DSM 797	DSM 797
  GCA_039525765.1	Rothia amarae	JCM 11375
  GCA_000307855.1	Schinkia azotoformans LMG 9581	LMG 9581
  GCA_017775145.1	Staphylococcus chromogenes	ATCC 43764
  GCA_014635745.1	Staphylococcus chromogenes	CCM 3387
  GCA_029024625.1	Staphylococcus chromogenes	DSM 20454
  GCA_900458195.1	Staphylococcus chromogenes	NCTC10530
  GCA_002901945.1	Staphylococcus chromogenes	NCTC 10530
  GCA_000875895.1	Staphylococcus gallinarum	DSM 20610
  GCA_900458615.1	Staphylococcus gallinarum	NCTC12195
  GCA_003968815.1	Staphylococcus gallinarum	NCTC 12195
  GCA_003019255.1	Staphylococcus kloosii	ATCC 43959
  GCA_900458805.1	Staphylococcus kloosii	NCTC12415
  GCA_002902055.1	Staphylococcus kloosii	NCTC 12415
  GCA_900167015.1	Succinivibrio dextrinosolvens DSM 3072	DSM 3072
  GCA_001270965.1	Sunxiuqinia dokdonensis	DH1
  GCA_900113005.1	Sunxiuqinia elliptica	CGMCC 1.9156
  GCA_001591425.1	Sutcliffiella cohnii NBRC 15565	NBRC 15565
  GCA_002019665.1	Sutcliffiella halmapala	DSM 8723
  GCA_001895205.1	Vibrio injensis	M12-1144
  GCA_001189575.1	Virgibacillus pantothenticus	DSM 26
  GCA_018075365.1	Virgibacillus pantothenticus	DSM 26
  GCA_900156795.1	Virgibacillus pantothenticus	DSM 26
  GCA_003148645.1	Xanthomarina spongicola	DSM 22637

이 내용은 strains_for_comp_analysis.txt 파일을 원본으로 한다. 이 파일의 첫 번째 컬럼(assembly accession)을 이용하여 FASTA file을 일괄적으로 다운로드하려면 다음의 복잡한 명령어를 이용하자. 세번째 줄은 내가 정말 좋아하는 스타일의 스크립트 조각('snippet')이다. 

  ncbi-genome-download -s genbank --formats fasta --flat-output \
      --output-folder OUTPUT \
      -A $(awk '{print $1}' strains_for_comp_analysis.txt | paste -sd, -) \
      bacteria

archaea 유전체를 다운로드하려면 맨 뒤의 groups를 bacteria에서 archaea로 고쳐 놓아야 한다. 가끔 에러 메시지 없이 다운로드가 되지 않는 경우가 있으니 잘 확인하기 바란다.