메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITIONS; AMINO ACID SUBSTITUTION; AUTOMATIC ANNOTATION; COMPLETE INFORMATION; EMPIRICAL APPROACH; HIER-ARCHICAL CLUSTERING; MULTIPLE ALIGNMENT; SUBSTITUTION MODELS;

EID: 44649194987     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-236     Document Type: Article
Times cited : (14)

References (43)
  • 1
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • 50453 1438297 10.1073/pnas.89.22.10915
    • Henikoff S Henikoff JG Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 1992, 89:10915-10919. 50453 1438297 10.1073/pnas.89.22.10915
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 3
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • 10.1089/10665270050514918 11382360
    • Muller T Vingron M Modeling amino acid replacement J Comput Biol 2000, 7:761-776. 10.1089/10665270050514918 11382360
    • (2000) J Comput Biol , vol.7 , pp. 761-776
    • Muller, T.1    Vingron, M.2
  • 4
    • 0346734129 scopus 로고    scopus 로고
    • The compositional adjustment of amino acid substitution matrices
    • 307629 14663142 10.1073/pnas.2533904100
    • Yu YK Wootton JC Altschul SF The compositional adjustment of amino acid substitution matrices Proc Natl Acad Sci USA 2003, 100:15688-15693. 307629 14663142 10.1073/pnas.2533904100
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15688-15693
    • Yu, Y.K.1    Wootton, J.C.2    Altschul, S.F.3
  • 5
    • 33646259688 scopus 로고    scopus 로고
    • Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins
    • 1459670 16607010 10.1128/EC.5.4.628-637.2006
    • Coronado JE Attie O Epstein SL Qiu WG Lipke PN Composition-modified matrices improve identification of homologs of saccharomyces cerevisiae low-complexity glycoproteins Eukaryot Cell 2006, 5:628-637. 1459670 16607010 10.1128/EC.5.4.628-637.2006
    • (2006) Eukaryot Cell , vol.5 , pp. 628-637
    • Coronado, J.E.1    Attie, O.2    Epstein, S.L.3    Qiu, W.G.4    Lipke, P.N.5
  • 6
    • 16344388556 scopus 로고    scopus 로고
    • The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
    • 10.1093/bioinformatics/bti070 15509610
    • Yu YK Altschul SF The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions Bioinformatics 2005, 21:902-911. 10.1093/bioinformatics/bti070 15509610
    • (2005) Bioinformatics , vol.21 , pp. 902-911
    • Yu, Y.K.1    Altschul, S.F.2
  • 7
    • 18144420835 scopus 로고    scopus 로고
    • Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions
    • 10.1016/j.crvi.2005.02.002 15948633
    • Bastien O Roy S Marechal E Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions C R Biol 2005, 328:445-453. 10.1016/j.crvi.2005.02.002 15948633
    • (2005) C R Biol , vol.328 , pp. 445-453
    • Bastien, O.1    Roy, S.2    Marechal, E.3
  • 8
    • 27144489108 scopus 로고    scopus 로고
    • Protein database searches using compositionally adjusted substitution matrices
    • 1343503 16218944 10.1111/j.1742-4658.2005.04945.x
    • Altschul SF Wootton JC Gertz EM Agarwala R Morgulis A Schaffer AA Yu YK Protein database searches using compositionally adjusted substitution matrices FEBS J 2005, 272:5101-5109. 1343503 16218944 10.1111/ j.1742-4658.2005.04945.x
    • (2005) FEBS J , vol.272 , pp. 5101-5109
    • Altschul, S.F.1    Wootton, J.C.2    Gertz, E.M.3    Agarwala, R.4    Morgulis, A.5    Schaffer, A.A.6    Yu, Y.K.7
  • 9
    • 0033670313 scopus 로고    scopus 로고
    • PHAT: A transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane
    • 10.1093/bioinformatics/16.9.760 11108698
    • Ng PC Henikoff JG Henikoff S PHAT: A transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane Bioinformatics 2000, 16:760-766. 10.1093/bioinformatics/16.9.760 11108698
    • (2000) Bioinformatics , vol.16 , pp. 760-766
    • Ng, P.C.1    Henikoff, J.G.2    Henikoff, S.3
  • 13
    • 0033181623 scopus 로고    scopus 로고
    • Molecular evolution of coding and non-coding regions in Plasmodium
    • 10697838
    • Pizzi E Frontali C Molecular evolution of coding and non-coding regions in Plasmodium Parassitologia 1999, 41:89-91. 10697838
    • (1999) Parassitologia , vol.41 , pp. 89-91
    • Pizzi, E.1    Frontali, C.2
  • 14
    • 0035220937 scopus 로고    scopus 로고
    • A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
    • RESEARCH0010 31479 11305938
    • Knight RD Freeland SJ Landweber LF A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes Genome Biol 2001, 2:RESEARCH0010. 31479 11305938
    • (2001) Genome Biol , pp. 2
    • Knight, R.D.1    Freeland, S.J.2    Landweber, L.F.3
  • 15
    • 0033977579 scopus 로고    scopus 로고
    • Increased coverage of protein families with the blocks database servers
    • 102407 10592233 10.1093/nar/28.1.228
    • Henikoff JG Greene EA Pietrokovski S Henikoff S Increased coverage of protein families with the blocks database servers Nucleic Acids Res 2000, 28:228-230. 102407 10592233 10.1093/nar/28.1.228
    • (2000) Nucleic Acids Res , vol.28 , pp. 228-230
    • Henikoff, J.G.1    Greene, E.A.2    Pietrokovski, S.3    Henikoff, S.4
  • 16
    • 0032776495 scopus 로고    scopus 로고
    • Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
    • 10.1093/bioinformatics/15.6.471 10383472
    • Henikoff S Henikoff JG Pietrokovski S Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations Bioinformatics 1999, 15:471-479. 10.1093/bioinformatics/15.6.471 10383472
    • (1999) Bioinformatics , vol.15 , pp. 471-479
    • Henikoff, S.1    Henikoff, J.G.2    Pietrokovski, S.3
  • 17
    • 0037466436 scopus 로고    scopus 로고
    • Low-complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations
    • 10.1016/S0166-6851(03)00039-2 12706793
    • Xue HY Forsdyke DR Low-complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations Mol Biochem Parasitol 2003, 128:21-32. 10.1016/S0166-6851(03)00039-2 12706793
    • (2003) Mol Biochem Parasitol , vol.128 , pp. 21-32
    • Xue, H.Y.1    Forsdyke, D.R.2
  • 18
    • 0037057374 scopus 로고    scopus 로고
    • Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    • RESEARCH0059. 133443 12429058 10.1186/gb-2002-3-11-research0059
    • Gasch AP Eisen MB Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering Genome Biol 2002, 3:RESEARCH0059. 133443 12429058 10.1186/gb-2002-3-11-research0059
    • (2002) Genome Biol , pp. 3
    • Gasch, A.P.1    Eisen, M.B.2
  • 20
    • 37849023306 scopus 로고    scopus 로고
    • Assessing performance of orthology detection strategies applied to eukaryotic genomes
    • 1849888 17440619 10.1371/journal.pone.0000383
    • Chen F Mackey AJ Vermunt JK Roos DS Assessing performance of orthology detection strategies applied to eukaryotic genomes PLoS ONE 2007, 2:e383. 1849888 17440619 10.1371/journal.pone.0000383
    • (2007) PLoS ONE , vol.2
    • Chen, F.1    Mackey, A.J.2    Vermunt, J.K.3    Roos, D.S.4
  • 21
    • 0032583111 scopus 로고    scopus 로고
    • Stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens
    • 10.1016/S0166-6851(98)00144-3
    • Cheng Q Cloonan N Fischer K Thompson J Waine G Lanzer M Saul A stevor and rif are Plasmodium falciparum multicopy gene families which potentially encode variant antigens Mol Biochem Parasitol 1998, 97:161-176. 10.1016/S0166-6851(98)00144-3 9879895
    • (1998) Mol Biochem Parasitol , vol.97 , pp. 161-176
    • Cheng, Q.1    Cloonan, N.2    Fischer, K.3    Thompson, J.4    Waine, G.5    Lanzer, M.6    Saul, A.7
  • 22
    • 34548319689 scopus 로고    scopus 로고
    • Variant proteins of the Plasmodium falciparum RIFIN family show distinct subcellular localization and developmental expression patterns
    • 10.1016/j.molbiopara.2007.07.011 17719658
    • Petter M Haeggstrom M Khattab A Fernandez V Klinkert MQ Wahlgren M Variant proteins of the Plasmodium falciparum RIFIN family show distinct subcellular localization and developmental expression patterns Mol Biochem Parasitol 2007, 156:51-61. 10.1016/j.molbiopara.2007.07.011 17719658
    • (2007) Mol Biochem Parasitol , vol.156 , pp. 51-61
    • Petter, M.1    Haeggstrom, M.2    Khattab, A.3    Fernandez, V.4    Klinkert, M.Q.5    Wahlgren, M.6
  • 24
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • 10.1016/S0168-9525(00)02024-2 10827456
    • Rice P Longden I Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends Genet 2000, 16:276-277. 10.1016/ S0168-9525(00)02024-2 10827456
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 26
    • 0035662252 scopus 로고    scopus 로고
    • Fine structure of Plasmodium falciparum subtelomeric sequences
    • 10.1016/S0166-6851(01)00362-0 11738715
    • Pizzi E Frontali C Fine structure of Plasmodium falciparum subtelomeric sequences Mol Biochem Parasitol 2001, 118:253-258. 10.1016/ S0166-6851(01)00362-0 11738715
    • (2001) Mol Biochem Parasitol , vol.118 , pp. 253-258
    • Pizzi, E.1    Frontali, C.2
  • 27
    • 0028836489 scopus 로고
    • Compositional properties of nuclear genes from Plasmodium falciparum
    • 10.1016/0378-1119(94)00708-Z 7828919
    • Musto H Rodriguez-Maseda H Bernardi G Compositional properties of nuclear genes from Plasmodium falciparum Gene 1995, 152:127-132. 10.1016/ 0378-1119(94)00708-Z 7828919
    • (1995) Gene , vol.152 , pp. 127-132
    • Musto, H.1    Rodriguez-Maseda, H.2    Bernardi, G.3
  • 28
    • 0033050538 scopus 로고    scopus 로고
    • Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection
    • 10.1007/PL00006531 10368431
    • Musto H Romero H Zavala A Jabbari K Bernardi G Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection J Mol Evol 1999, 49:27-35. 10.1007/PL00006531 10368431
    • (1999) J Mol Evol , vol.49 , pp. 27-35
    • Musto, H.1    Romero, H.2    Zavala, A.3    Jabbari, K.4    Bernardi, G.5
  • 29
    • 3042830466 scopus 로고    scopus 로고
    • Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference
    • 10.1016/j.gene.2004.04.029 15246528
    • Bastien O Lespinats S Roy S Metayer K Fertil B Codani JJ Marechal E Analysis of the compositional biases in Plasmodium falciparum genome and proteome using Arabidopsis thaliana as a reference Gene 2004, 336:163-173. 10.1016/j.gene.2004.04.029 15246528
    • (2004) Gene , vol.336 , pp. 163-173
    • Bastien, O.1    Lespinats, S.2    Roy, S.3    Metayer, K.4    Fertil, B.5    Codani, J.J.6    Marechal, E.7
  • 30
    • 0035104190 scopus 로고    scopus 로고
    • Low-complexity regions in Plasmodium falciparum proteins
    • 311019 11157785 10.1101/gr.GR-1522R
    • Pizzi E Frontali C Low-complexity regions in Plasmodium falciparum proteins Genome Res 2001, 11:218-229. 311019 11157785 10.1101/gr.GR-1522R
    • (2001) Genome Res , vol.11 , pp. 218-229
    • Pizzi, E.1    Frontali, C.2
  • 31
    • 0032778047 scopus 로고    scopus 로고
    • The genomic tree as revealed from whole proteome comparisons
    • 310764 10400922
    • Tekaia F Lazcano A Dujon B The genomic tree as revealed from whole proteome comparisons Genome Res 1999, 9:550-557. 310764 10400922
    • (1999) Genome Res , vol.9 , pp. 550-557
    • Tekaia, F.1    Lazcano, A.2    Dujon, B.3
  • 32
    • 0033563471 scopus 로고    scopus 로고
    • Applications of the pyramidal clustering method to biological objects
    • 10.1016/S0097-8485(99)00006-6 10404622
    • Aude JC az-Lazcoz Y Codani JJ Risler JL Applications of the pyramidal clustering method to biological objects Comput Chem 1999, 23:303-315. 10.1016/S0097-8485(99)00006-6 10404622
    • (1999) Comput Chem , vol.23 , pp. 303-315
    • Aude, J.C.1    Az-Lazcoz, Y.2    Codani, J.J.3    Risler, J.L.4
  • 33
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • 1347485 16381887 10.1093/nar/gkj123
    • Chen F Mackey AJ Stoeckert CJ Jr Roos DS OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups Nucleic Acids Res 2006, 34:D363-D368. 1347485 16381887 10.1093/nar/gkj123
    • (2006) Nucleic Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert Jr., C.J.3    Roos, D.S.4
  • 34
    • 39849095227 scopus 로고    scopus 로고
    • Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family
    • 2257938 18197962 10.1186/1471-2164-9-19
    • Joannin N Abhiman S Sonnhammer EL Wahlgren M Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family BMC Genomics 2008, 9:19. 2257938 18197962 10.1186/1471-2164-9-19
    • (2008) BMC Genomics , vol.9 , pp. 19
    • Joannin, N.1    Abhiman, S.2    Sonnhammer, E.L.3    Wahlgren, M.4
  • 36
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: Automated segmentation using complexity measures
    • 10.1016/0097-8485(94)85023-2 7952898
    • Wootton JC Non-globular domains in protein sequences: Automated segmentation using complexity measures Comput Chem 1994, 18:269-285. 10.1016/0097-8485(94)85023-2 7952898
    • (1994) Comput Chem , vol.18 , pp. 269-285
    • Wootton, J.C.1
  • 37
    • 84888275631 scopus 로고    scopus 로고
    • ftp://ftp.ncbi.nih.gov/repository/blocks/unix/old/blocks-14.1
    • BLOCKS Database ftp://ftp.ncbi.nih.gov/repository/blocks/unix/old/ blocks-14.1
    • BLOCKS Database
  • 38
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • 29669 11139604 10.1093/nar/29.2.351
    • Altschul SF Bundschuh R Olsen R Hwa T The estimation of statistical parameters for local alignment score distributions Nucleic Acids Res 2001, 29:351-361. 29669 11139604 10.1093/nar/29.2.351
    • (2001) Nucleic Acids Res , vol.29 , pp. 351-361
    • Altschul, S.F.1    Bundschuh, R.2    Olsen, R.3    Hwa, T.4
  • 39
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 146917 9254694 10.1093/nar/25.17.3389
    • Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.