proA:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0244, b0243, JW0233, pro1, pro(1)''<ref name='LIB:Riley_2006'/>
''ECK0244, b0243, JW0233, pro1, pro(1)''<ref name='LIB:Riley_2006'/>, pro''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9aba3431ee"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10767 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10767 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|259727|262980|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|259727|262980|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|260727|261980|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|260727|261980|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10767 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10767 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|260726|NC_261979|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|260726|261979|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|260726|NC_261979|FASTA Dump}}  
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W3110: 260727..261980<br /><gbrowseImage>
W3110: 260727..261980<br /><gbrowseImage>
name=AC_000091:260727..261980
name=NC_007779:260727..261980
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|259727|262980|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|259727|262980|GBrowse(W3110)}}  
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DH10B: 234831..236084<br /><gbrowseImage>
DH10B: 234831..236084<br /><gbrowseImage>
name=NC_010473:234831..236084
name=NC_010473:234831..236084
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|232325|238590|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|232325|238590|GBrowse(DH10B)}}
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{|   id="D46a9aba4440d7"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9aba4440d7"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="P46a9aba4b525d"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P46a9aba4b525d"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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''proA''
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Resistant to
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Resistant to Nitro(4)pyridine N-oxide
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PMID:4598010
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''proA''
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Resistant to
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Nitro-4-pyridine N-oxide Resistance
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PMID:385587
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Strain: W3630
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table 1


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{|   id="Y4e04c17f26673"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y4e04c17f26673"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCCGCACGAATGGTGTAATCACC  
Primer 2:CCCGCACGAATGGTGTAATCACC  
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[[:Category:Kohara_Phage:8F9|8F9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=127 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:8G4|8G4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=128 Genobase]
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PMID:3038334
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{|   id="Z46a9aba691c43"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9aba691c43"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10767 EcoCyc:EG10767]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0760 EchoBASE:EB0760]
EcoCyc:EG10767
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0243 EcoliGenExpDB:b0243]
EcoGene:EG10767
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0390 ECOL199310CYC:C0390]
RegulonDB:ECK120000758
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10767 EcoGene:EG10767]
[http://www.ncbi.nlm.nih.gov/gene?term=946680 GeneID:946680]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=PROA ECOO157CYC:PROA]
EchoBASE:EB0760
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/364 CGSC:364]
ASAP:ABE-0000832
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000832&formSubmitReturn=1 ASAP:ABE-0000832]
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!|Name!!URL!!Comments
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Latest revision as of 20:28, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

proA

Mnemonic

Proline

Synonyms

ECK0244, b0243, JW0233, pro1, pro(1)[1], pro

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

5.62 minutes 

MG1655: 260727..261980
<gbrowseImage> name=NC_000913:260727..261980 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 265995..267248
<gbrowseImage> name=NC_012967:265995..267248 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 260726..261979
<gbrowseImage> name=NC_012759:260726..261979 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 260727..261980
<gbrowseImage> name=NC_007779:260727..261980 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 234831..236084
<gbrowseImage> name=NC_010473:234831..236084 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

260727

Edman degradation

PMID:6089111[2]


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔproA (Keio:JW0233)

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

Shigen

CGSC8468[4]

proA::Tn5KAN-2 (FB20067)

Insertion at nt 192 in Plus orientation

Auxotrophies

Requires proline for growth

PMID:15262929[5]

E. coli Genome Project:FB20067

does not contain pKD46

proA81::Tn10

Insertion at 261,286 bp in MG1655 (NC_000913)

Auxotrophies

Requires proline for growth

adapted from Nichols et al.[6]

CAG18447 = CGSC7330[4]

Synonyms:

proA761(del)::kan

insertion

insertion

Auxotrophies

Requires proline for growth

proA23

Auxotrophies

Requires proline for growth

CGSC:5573

proA44

Auxotrophies

Requires proline for growth

CGSC:6453

proA81::Tn10

Auxotrophies

Requires proline for growth

PMID:9829956[7]

CGSC:7088

proA35

Auxotrophies

Requires proline for growth

CGSC:8556

proA30

Auxotrophies

Requires proline for growth

CGSC:11535

proA181

Auxotrophies

Requires proline for growth

CGSC:12290

proA180

Auxotrophies

Requires proline for growth

CGSC:12291

proA

Auxotrophies

Requires proline for growth

CGSC:14522

proA3096::Tn10kan

Auxotrophies

Requires proline for growth

PMID:2540407[8] PMID:9829956[7]

CGSC:38994

ΔproA761::kan

deletion

deletion

Auxotrophies

Requires proline for growth

PMID:16738554[3]

CGSC:102466

proA

Resistant to

Resistant to Nitro(4)pyridine N-oxide

PMID:4598010[9]

proA

Resistant to

Nitro-4-pyridine N-oxide Resistance

PMID:385587[10]

Strain: W3630

table 1

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0233

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCCTGGAACAAATGGGCATTGC

Primer 2:CCCGCACGAATGGTGTAATCACC

8F9

Kohara Phage

Genobase

PMID:3038334[12]

8G4

Kohara Phage

Genobase

PMID:3038334[12]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[4]

est. P1 cotransduction: 33% [6]
Synonyms:zae-502::Tn10

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[4]

est. P1 cotransduction: % [6]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10767

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10767

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000758

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946680

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0760

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000832

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Deutch, AH et al. (1984) Analysis of the Escherichia coli proBA locus by DNA and protein sequencing. Nucleic Acids Res. 12 6337-55 PubMed
  3. ↑ 3.0 3.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  4. ↑ 4.0 4.1 4.2 4.3 CGSC: The Coli Genetics Stock Center
  5. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 6.0 6.1 6.2 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ 7.0 7.1 Nichols, BP et al. (1998) Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J. Bacteriol. 180 6408-11 PubMed
  8. ↑ Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  9. ↑ Berg, CM & Rossi, JJ (1974) Proline excretion and indirect suppression in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 118 928-34 PubMed
  10. ↑ Fayerman, JT et al. (1979) ilvU, a locus in Escherichia coli affecting the derepression of isoleucyl-tRNA synthetase and the RPC-5 chromatographic profiles of tRNAIle and tRNAVal. J. Biol. Chem. 254 9429-40 PubMed
  11. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  12. ↑ 12.0 12.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed

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