메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

Software for the analysis and visualization of deep mutational scanning data

Author keywords

Amino acid preferences; Deep mutational scanning; Sequence logo

Indexed keywords

AMINO ACIDS; SCANNING; SITE SELECTION; VISUALIZATION;

EID: 84930207201     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0590-4     Document Type: Article
Times cited : (92)

References (40)
  • 1
    • 84905217368 scopus 로고    scopus 로고
    • Deep mutational scanning: a new style of protein science
    • Fowler DM, Fields S. Deep mutational scanning: a new style of protein science. Nat Methods. 2014; 11(8):801-7.
    • (2014) Nat Methods , vol.11 , Issue.8 , pp. 801-807
    • Fowler, D.M.1    Fields, S.2
  • 3
    • 84867069553 scopus 로고    scopus 로고
    • Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing
    • Traxlmayr MW, Hasenhindl C, Hackl M, Stadlmayr G, Rybka JD, Borth N, et al.Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing. J Mol Biol. 2012; 423:397-412.
    • (2012) J Mol Biol. , vol.423 , pp. 397-412
    • Traxlmayr, M.W.1    Hasenhindl, C.2    Hackl, M.3    Stadlmayr, G.4    Rybka, J.D.5    Borth, N.6
  • 5
    • 84875870975 scopus 로고    scopus 로고
    • Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis
    • Starita LM, Pruneda JN, Lo RS, Fowler DM, Kim HJ, Hiatt JB, et al. Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis. Proc Natl Acad Sci USA. 2013; 110(14):1263-72.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.14 , pp. 1263-1272
    • Starita, L.M.1    Pruneda, J.N.2    Lo, R.S.3    Fowler, D.M.4    Kim, H.J.5    Hiatt, J.B.6
  • 6
    • 84886037483 scopus 로고    scopus 로고
    • Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly (A)-binding protein
    • Melamed D, Young DL, Gamble CE, Miller CR, Fields S. Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly (A)-binding protein. RNA. 2013; 19(11):1537-51.
    • (2013) RNA , vol.19 , Issue.11 , pp. 1537-1551
    • Melamed, D.1    Young, D.L.2    Gamble, C.E.3    Miller, C.R.4    Fields, S.5
  • 7
    • 84875703570 scopus 로고    scopus 로고
    • Analyses of the effects of all ubiquitin point mutants on yeast growth rate
    • Roscoe BP, Thayer KM, Zeldovich KB, Fushman D, Bolon DN. Analyses of the effects of all ubiquitin point mutants on yeast growth rate. J Mol Biol. 2013; 425:1363-77.
    • (2013) J Mol Biol. , vol.425 , pp. 1363-1377
    • Roscoe, B.P.1    Thayer, K.M.2    Zeldovich, K.B.3    Fushman, D.4    Bolon, D.N.5
  • 8
    • 84901408859 scopus 로고    scopus 로고
    • A comprehensive, high-resolution map of a gene's fitness landscape
    • Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol. 2014; 31(6):1581-92.
    • (2014) Mol Biol Evol , vol.31 , Issue.6 , pp. 1581-1592
    • Firnberg, E.1    Labonte, J.W.2    Gray, J.J.3    Ostermeier, M.4
  • 9
    • 84905001681 scopus 로고    scopus 로고
    • An experimentally determined evolutionary model dramatically improves phylogenetic fit
    • Bloom JD. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol. 2014; 30:1956-78. http://mbe.oxfordjournals.org/content/31/8/1956 .
    • (2014) Mol Biol Evol , vol.30 , pp. 1956-1978
    • Bloom, J.D.1
  • 10
    • 84906217475 scopus 로고    scopus 로고
    • Comprehensive mutational scanning of a kinase in vivo reveals context-dependent fitness landscapes
    • Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS. Comprehensive mutational scanning of a kinase in vivo reveals context-dependent fitness landscapes. Nucleic Acids Res. 2014; 42:112.
    • (2014) Nucleic Acids Res , vol.42 , pp. 112
    • Melnikov, A.1    Rogov, P.2    Wang, L.3    Gnirke, A.4    Mikkelsen, T.S.5
  • 11
    • 84905197658 scopus 로고    scopus 로고
    • The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
    • Thyagarajan B, Bloom JD. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. eLife. 2014; 3:03300. http://elifesciences.org/content/3/e03300 .
    • (2014) eLife , vol.3 , pp. 03300
    • Thyagarajan, B.1    Bloom, J.D.2
  • 12
    • 84900431101 scopus 로고    scopus 로고
    • High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution
    • Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, et al. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution. Sci Rep. 2014; 4:4942.
    • (2014) Sci Rep , vol.4 , pp. 4942
    • Wu, N.C.1    Young, A.P.2    Al-Mawsawi, L.Q.3    Olson, C.A.4    Feng, J.5    Qi, H.6
  • 13
    • 84910670272 scopus 로고    scopus 로고
    • High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment
    • 10157-64
    • Wu NC, Young AP, Al-Mawsawi LQ, Olson CA, Feng J, Qi H, et al. High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment. J Virol. 2014; 88(17):10157-64.
    • (2014) J Virol , vol.88 , Issue.17
    • Wu, N.C.1    Young, A.P.2    Al-Mawsawi, L.Q.3    Olson, C.A.4    Feng, J.5    Qi, H.6
  • 14
    • 84923249936 scopus 로고    scopus 로고
    • A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain
    • Olson CA, Wu NC, Sun R. A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. Curr Biol. 2014; 24(22):2643-51.
    • (2014) Curr Biol , vol.24 , Issue.22 , pp. 2643-2651
    • Olson, C.A.1    Wu, N.C.2    Sun, R.3
  • 16
    • 84871288267 scopus 로고    scopus 로고
    • PFunkel: efficient, expansive, user-defined mutagenesis
    • Firnberg E, Ostermeier M. PFunkel: efficient, expansive, user-defined mutagenesis. PLoS One. 2012; 7:52031.
    • (2012) PLoS One , vol.7 , pp. 52031
    • Firnberg, E.1    Ostermeier, M.2
  • 17
    • 84892698156 scopus 로고    scopus 로고
    • A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library
    • Jain PC, Varadarajan R. A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. Anal Biochem. 2014; 449:90-8.
    • (2014) Anal Biochem , vol.449 , pp. 90-98
    • Jain, P.C.1    Varadarajan, R.2
  • 18
    • 84907257107 scopus 로고    scopus 로고
    • Saturation editing of genomic regions by multiplex homology-directed repair
    • Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nat. 2014; 513(7516):120-3.
    • (2014) Nat , vol.513 , Issue.7516 , pp. 120-123
    • Findlay, G.M.1    Boyle, E.A.2    Hause, R.J.3    Klein, J.C.4    Shendure, J.5
  • 19
    • 83355174920 scopus 로고    scopus 로고
    • Enrich: software for analysis of protein function by enrichment and depletion of variants
    • Fowler DM, Araya CL, Gerard W, Fields S. Enrich: software for analysis of protein function by enrichment and depletion of variants. Bioinformatics. 2011; 27(24):3430-1.
    • (2011) Bioinformatics , vol.27 , Issue.24 , pp. 3430-3431
    • Fowler, D.M.1    Araya, C.L.2    Gerard, W.3    Fields, S.4
  • 20
    • 84895727363 scopus 로고    scopus 로고
    • A bayesian mcmc approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments
    • Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. A bayesian mcmc approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments. Genet. 2014; 196(3):841-52.
    • (2014) Genet , vol.196 , Issue.3 , pp. 841-852
    • Bank, C.1    Hietpas, R.T.2    Wong, A.3    Bolon, D.N.4    Jensen, J.D.5
  • 21
    • 84867644046 scopus 로고    scopus 로고
    • A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
    • 16858-63
    • Araya CL, Fowler DM, Chen W, Muniez I, Kelly JW, Fields S. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc Natl Acad Sci. 2012; 109(42):16858-63.
    • (2012) Proc Natl Acad Sci , vol.109 , Issue.42
    • Araya, C.L.1    Fowler, D.M.2    Chen, W.3    Muniez, I.4    Kelly, J.W.5    Fields, S.6
  • 22
    • 84922384542 scopus 로고    scopus 로고
    • A systematic survey of an intragenic epistatic landscape
    • Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol. 2015; 32(1):229-38.
    • (2015) Mol Biol Evol , vol.32 , Issue.1 , pp. 229-238
    • Bank, C.1    Hietpas, R.T.2    Jensen, J.D.3    Bolon, D.N.4
  • 23
    • 77449144323 scopus 로고    scopus 로고
    • Parallel, tag-directed assembly of locally derived short sequence reads
    • Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods. 2010; 7(2):119-22.
    • (2010) Nat Methods , vol.7 , Issue.2 , pp. 119-122
    • Hiatt, J.B.1    Patwardhan, R.P.2    Turner, E.H.3    Lee, C.4    Shendure, J.5
  • 25
    • 84923357744 scopus 로고    scopus 로고
    • An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs
    • Bloom JD. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol. 2014; 31:2753-769. http://mbe.oxfordjournals.org/content/31/10/2753 .
    • (2014) Mol Biol Evol , vol.31 , pp. 2753-2769
    • Bloom, J.D.1
  • 26
    • 25444482352 scopus 로고    scopus 로고
    • The exchangeability of amino acids in proteins
    • Yampolsky LY, Stoltzfus A. The exchangeability of amino acids in proteins. Genet. 2005; 170(4):1459-72.
    • (2005) Genet , vol.170 , Issue.4 , pp. 1459-1472
    • Yampolsky, L.Y.1    Stoltzfus, A.2
  • 27
    • 69249205499 scopus 로고    scopus 로고
    • Climbing mount probable: mutation as a cause of nonrandomness in evolution
    • Stoltzfus A, Yampolsky LY. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J Hered. 2009; 100(5):637-47.
    • (2009) J Hered , vol.100 , Issue.5 , pp. 637-647
    • Stoltzfus, A.1    Yampolsky, L.Y.2
  • 28
    • 0000629281 scopus 로고
    • Mathematical contributions to the theory of evolution. On a form of spurious correlation which may arise when indices are used in the measurement of organs
    • Pearson K. Mathematical contributions to the theory of evolution. On a form of spurious correlation which may arise when indices are used in the measurement of organs. Proc Royal Society London. 1896; 60(359-367):489-98.
    • (1896) Proc Royal Society London , vol.60 , Issue.359-367 , pp. 489-498
    • Pearson, K.1
  • 29
    • 0004770050 scopus 로고
    • On the constants of index-distributions as deduced from the like constants for the components of the ratio, with special reference to the opsonic index
    • Pearson K. On the constants of index-distributions as deduced from the like constants for the components of the ratio, with special reference to the opsonic index. Biometrika. 1910; 7(4):531-41. doi:10.1093/biomet/7.4.531.
    • (1910) Biometrika , vol.7 , Issue.4 , pp. 531-541
    • Pearson, K.1
  • 31
    • 0034175543 scopus 로고    scopus 로고
    • Mean and variance of ratio estimators used in fluorescence ratio imaging
    • Van Kempen G, Van Vliet L. Mean and variance of ratio estimators used in fluorescence ratio imaging. Cytometry. 2000; 39(4):300-5.
    • (2000) Cytometry , vol.39 , Issue.4 , pp. 300-305
    • Van Kempen, G.1    Van Vliet, L.2
  • 32
    • 84930212284 scopus 로고    scopus 로고
    • PyStan: the Python interface to Stan, Version 2.5.0.
    • Stan Development Team. PyStan: the Python interface to Stan, Version 2.5.0. 2014. http://mc-stan.org/pystan.html .
    • (2014)
  • 33
    • 84972492387 scopus 로고
    • Inference from iterative simulation using multiple sequences
    • Gelman A, Rubin DB. Inference from iterative simulation using multiple sequences. Stat Sci. 1992; 7:457-72.
    • (1992) Stat Sci , vol.7 , pp. 457-472
    • Gelman, A.1    Rubin, D.B.2
  • 34
  • 35
    • 84921873998 scopus 로고    scopus 로고
    • Points of significance: replication
    • Blainey P, Krzywinski M, Altman N. Points of significance: replication. Nat Methods. 2014; 11(9):879-80.
    • (2014) Nat Methods , vol.11 , Issue.9 , pp. 879-880
    • Blainey, P.1    Krzywinski, M.2    Altman, N.3
  • 36
    • 0021968408 scopus 로고
    • Genetic analysis of staphylococcal nuclease: identification of three intragenic "global" suppressors of nuclease-minus mutations
    • Shortle D, Lin B. Genetic analysis of staphylococcal nuclease: identification of three intragenic "global" suppressors of nuclease-minus mutations. Genet. 1985; 110:539-55.
    • (1985) Genet , vol.110 , pp. 539-555
    • Shortle, D.1    Lin, B.2
  • 38
    • 0030737949 scopus 로고    scopus 로고
    • Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization
    • Shafikhani S, Siegel RA, Ferrari E, Schellenberger V. Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. Biotechniques. 1997; 23:304-10.
    • (1997) Biotechniques , vol.23 , pp. 304-310
    • Shafikhani, S.1    Siegel, R.A.2    Ferrari, E.3    Schellenberger, V.4
  • 39
    • 3042681604 scopus 로고    scopus 로고
    • Protein tolerance to random amino acid change
    • Guo HH, Choe J, Loeb LA. Protein tolerance to random amino acid change. Proc Natl Acad Sci USA. 2004; 101:9205-210.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9205-9210
    • Guo, H.H.1    Choe, J.2    Loeb, L.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.