PIR-ALN: A database of protein sequence alignments

Bioinformatics

Volumn 15, Issue 5, 1999, Pages 382-390

  Srinivasarao, Geetha Y ^a   Yeh, Lai Su L ^a   Marzec, Christopher R ^a   Orcutt, Bruce C ^a   Barker, Winona C ^a  

^a National Biomedical Research Foundation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL NEURAL NETWORK; DATA BASE; INFORMATION RETRIEVAL; INTERNET; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

EID: 0033030856     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.5.382     Document Type: Article

References (63)

1. Aberle, H., Schwartz, H., Hoschuetzky, H. and Kemler, R. (1996) Single amino acid substitutions in proteins of the armadillo gene family abolish their binding to alpha-catenin. J. Biol. Chem., 271, 1520-1526.
2. Adzhubei, I.A., Adzhubei, A.A. and Neidle, S. (1998) An integrated sequence-structure database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data. Nucleic Acids Res., 26, 327-331.
3. Alkema, M.J., Bronk, M., Verhoeven, E., Otte, A., van 't Veer, L.J., Berns, A. and van Lohuizen, M. (1997) Identification of Bmil-interacting proteins as constituents of a multimeric mammalian polycomb complex. Genes Dev., 11, 226-240.
4. Attwood, T., Payne, A.W.R., Michie, A.D. and Parry-Smith, D.J. (1997) A Colour INteractive Editor for Multiple Alignments - CINEMA. EMBnet.news, 3 (http://www2.ebi.ac.uk/embnet/news/).
5. Attwood, T.K., Beck, M.E., Flower, D.R., Scordis, P. and Selley, J.N. (1998) The PRINTS protein fingerprint database in its fifth year. Nucleic Acids Res., 26, 304-308.
6. Bachinsky, A.G., Yarigin, A.A., Guseva, E.H., Kulichkov, V.A. and Nizolenko, L.Ph. (1997) A bank of protein family patterns for rapid identification of possible functions of amino acid sequences. Comput. Applic. Biosci., 13, 115-122.
7. Bairoch, A. (1993) The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res., 21, 3097-3103.
8. Barker, W.C., George, D.G., Srinivasarao, G.Y. and Yeh, L.-S. (1992) Database of protein sequence alignments. FASEB J., 6, A348.
9. Barker, W.C., George, D.G., Mewes, H.-W., Pfeiffer, F. and Tsugita, A. (1993) The PIR-International databases. Nucleic Acids Res., 21, 3089-3092.
10. Barker, W.C., Pfeiffer, F. and George, D.G. (1995) Superfamily and domain: organization of data for molecular evolution studies. In Atassi, M.Z. and Appella, E. (eds). Methods in Protein Structure Analysis. Plenum Press, New York, pp. 473-481.
11. Barker, W.C., Pfeiffer, F. and George, D.G. (1996) Superfamily classification in PIR-International Protein Sequence Database. Methods Enzymol., 266, 59-71.
12. Barker, W.C. et al. (1999) The PIR-International Protein Sequence Database. Nucleic Acids Res., 27, 39-43.
13. Baron, M., Norman, D.G. and Campbell, I.D. (1991) Protein modules. Trends Biochem. Sci., 16, 13-17.
14. Benner, S.A., Cohen, M.A. and Gonnet, G.H. (1994) Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng., 7, 1323-1332.
15. Bilaud, T., Koering, C.E., Binet-Brasselet, E., Ancelin, K., Pollice, A., Gasser, S.M. and Gilson, E. (1996) The telobox, a Myb-related telomeric DNA binding motif found in proteins from yeast, plants and human. Nucleic Acids Res., 24, 1294-1303.
16. Bork, P. (1991) Shuffled domains in extracellular proteins. FEBS Lett., 286, 47-54.
17. Bork, P., Downing, A.K., Kieffer, B. and Campbell, I.D. (1996) Structure and distribution of modules in extracellular proteins. Q. Rev. Biophys., 29, 119-167.
18. Brown, S.M. (1998) Analyzing protein families and domains on the Web. BioTechniques, 25, 596-598.
19. Chuang, M.-H., Pan, F.-M. and Chiou, S.-H. (1997) Sequence characterization of gamma-crystallins from lip shark (Chiloscyllium colax): Existence of two cDNAs encoding gamma-crystallins of mammalian and teleostean classes. J. Protein Chem., 16, 299-307.
20. Clark, S.P. (1992) MALIGNED: a multiple sequence alignment editor. Comput. Applic. Biosci., 8, 535-538.
21. Cosman, D., Lyman, S.D., Idzerda, R.L., Beckmann, M.P., Park, L.S., Goodwin, R.G. and March, C.J. (1990) A new cytokine receptor superfamily. Trends Biochem. Sci., 15, 265-270.
22. Dayhoff, M.O. (1976) The origin and evolution of protein superfamilies. Fed. Proc., 35, 2132-2138.
23. Dayhoff, M.O., McLaughlin, P.J., Barker, W.C. and Hunt, L.T. (1975) Evolution of sequences within protein superfamilies. Naturwissenschaften, 61, 154-161.
24. Depiereux, E. and Feytmans, E. (1992) MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Applic. Biosci., 8, 501-509.
25. Dodge, C., Schneider, R. and Sander, C. (1998) The HSSP database of protein structure - sequence alignments and family profiles. Nucleic Acids Res., 26, 313-315.
26. Doolittle, R.F. (1995) The multiplicity of domains in proteins. Annu. Rev. Biochem., 64, 287-314.
27. Dosanjh, M.K., Collins, D.W., Fan, W., Lennon, G.G., Albala, J.S., Shen, Z. and Schild, D. (1998) Isolation and characterization of RAD51C, a new human member of the RAD51 family of related genes. Nucleic Acids Res., 26, 1179-1184.
28. Douglas, D.A., Shi, Y.E. and Sang, Q.A. (1997) Computational sequence analysis of the tissue inhibitor of metalloproteinase family. J. Protein Chem., 16, 237-255.
29. Emery, P., Durand, B., Mach, B. and Reith, W. (1996) RFX proteins, a novel family of DNA binding proteins conserved in the eukaryotic kingdom. Nucleic Acids Res., 24, 803-807.
30. Fiordalisi, J.J., Al-Rabiee, R., Chiappinelli, V.A. and Grant, G.A. (1994) Site-directed mutagenesis of kappa-bungarotoxin: implications for neuronal receptor specificity. Biochemistry, 33, 3872-3877.
31. Gribskov, M. and Veretnik, S. (1996) Identification of sequence patterns with profile analysis. Methods Enzymol., 266, 198-212.
32. Häger, K.-P., Braun, H., Czihal, A., Müller, B. and Bäumlein, H. (1995) Evolution of seed storage protein genes: Legumin genes of Ginkgo biloba. J. Mol. Evol., 41, 457-466.
33. Henikoff, J.G. and Henikoff, S. (1996) Blocks database and its applications. Methods Enzymol., 266, 88-105.
34. Henikoff, S., Endow, S.A. and Greene, E.A. (1996) Connecting protein family resources using the proWeb network. Trends Biochem. Sci., 21, 444-445.
35. Henrique, D., Tyler, D., Kintner, C., Heath, J.K., Lewis, J.H., Ish-Horowicz, D. and Storey, K.G. (1997) cash4. a novel achaete-scute homolog induced by Hensen's node during generation of the posterior nervous system. Genes Dev., 11, 603-615.
36. Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput. Applic. Biosci., 8, 189-191.
37. Hofmann, K. (1998) Protein classification & functional assignment. Trends Guide To Bioinformatics, (Trends Supplement), 18-21.
38. Hunt, L.T. (1987) Protein Identification Resource Newsletter, No. 3., National Biomedical Research Foundation, Washington, DC.
39. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci., 8, 275-282.
40. Kanai, S., Kikuno, R., Toh, H., Ryo, H. and Todo, T. (1997) Molecular evolution of the photolyase-blue-light photoreceptor family. J. Mol. Evol., 45, 535-548.
41. Matsuo, Y., Yamada, A., Tsukamoto, K., Tamura, H.-O., Ikezawa, H., Nakamura, H. and Nishikawa, K. (1996) A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I. Protein Sci., 5, 2459-2467.
42. McClure, M.A., Vasi, T.K. and Fitch, W.M. (1994) Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol., 11, 571-592.
43. Meinnel, T., Lazennec, C., Villoing, S. and Blanquet, S. (1997) Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion. J. Mol. Biol., 267, 749-761.
44. Mewes, H.-W., Albermann, K., Heumann, K., Liebl, S. and Pfeiffer, F. (1997) MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res., 25, 28-30.
45. Neuwald, A.F., Liu, J.S., Lipman, D.J. and Lawrence, C.E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res., 25, 1665-1677.
46. Nevill-Manning, C.G., Wu, T.D. and Brutlag, D.L. (1998) Highly specific protein sequence motifs for genome analysis. Proc. Natl Acad. Sci. USA, 95, 5865-5871.
47. Patthy, L. (1991) Modular exchange principles in proteins. Curr. Opin. Struct. Biol., 1, 351-361.
48. Ponting, C.P. (1997) Tudor domains in proteins that interact with RNA. Trends Biochem. Sci., 22, 51-52.
49. Schuler, G.D., Altschul, S.F. and Lipman, D.J. (1991) A workbench for multiple alignment construction and analysis. Proteins, 9, 180-190.
50. Schultz, J., Ponting, C.P., Hofmann, K. and Bork, P. (1997) SAM as a protein interaction domain involved in developmental regulation. Protein Sci., 6, 249-253.
51. Schultz, J., Milpetz, F., Bork, P. and Ponting, C.P. (1998) SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl Acad. Sci. USA, 95, 5857-5864.
52. Siezen, R.J. and Leunissen, J.A.M. (1997) Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci., 6, 501-523.
53. Smith, C.M., Shindyalov, I.N., Veretnik, S., Gribskov, M., Taylor, S.S., Ten Eyck, L.F. and Bourne, P.E. (1997) The protein kinase resource. Trends Biochem. Sci., 22, 444-446.
54. Smith, S.W., Overbeek, R., Woese, C.R., Gilbert, W. and Gillevet, P.M. (1994) The genetic data environment an expandable GUI for multiple sequence analysis. Comput. Applic. Biosci., 10, 671-675.
55. Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A. and Durbin, R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res., 26, 320-322.
56. Srinivasarao, G.Y., George, D.G. and Barker, W.C. (1990) The 1989 mutation data matrix. Biophys. J., 57, 429a.
57. Srinivasarao, G.Y., Yeh, L.-S., Marzec, C.R., Orcutt, B.C., Barker, W.C. and Pfeiffer, F. (1999) Database of protein sequence alignments: PIR-ALN. Nucleic Acids Res., 27, 284-285.
58. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
59. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
60. Wissmann, A., Ingles, J., McGhee, J.D. and Mains, P.E. (1997) Caenorhabditis elegans LET-502 is related to Rho-binding kinases and human myotonic dystrophy kinase and interacts genetically with a homolog of the regulatory subunit of smooth muscle myosin phosphatase to affect cell shape. Genes Dev., 11, 409-422.
61. Wu, C.H., Shivakumar, S., Shivakumar, C.V. and Chen, S.-C. (1998) GeneFIND Web server for protein family identification and information retrieval. Bioinformatics, 14, 223-224.
62. Yeh, L.-S., Srinivasarao, G.Y. and Barker, W.C. (1993a) Multiple sequence alignment methods. Biophys. J., 64, A220.
63. Yeh, L.-S., Srinivasarao, G.Y. and Barker, W.C. (1993b) A study of multiple sequence alignment methods. Fifth International Symposium and Workshops, June 15-20, Baltimore, MD, USA.