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Volumn 2, Issue DEC, 2008, Pages

A Python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites

Author keywords

Bioinformatics; Machine learning; Neuropeptides; Precursor cleavage; Python; Rhesus monkey; Support vector machine

Indexed keywords


EID: 67650817831     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/neuro.11.007.2008     Document Type: Article
Times cited : (21)

References (25)
  • 2
    • 33646543701 scopus 로고    scopus 로고
    • Bridging neuropeptidomics and genomics with bioinformatics: Prediction of mammalian neuropeptide prohormone processing
    • Amare, A., Hummon, A. B., Southey, B. R., Zimmerman, T. A., Rodriguez- Zas, S. L., and Sweedler, J. V. (2006). Bridging neuropeptidomics and genomics with bioinformatics: prediction of mammalian neuropeptide prohormone processing. J. Proteome Res. 5, 1162-1167.
    • (2006) J. Proteome Res , vol.5 , pp. 1162-1167
    • Amare, A.1    Hummon, A.B.2    Southey, B.R.3    Zimmerman, T.A.4    Rodriguez-Zas, S.L.5    Sweedler, J.V.6
  • 3
    • 36948999784 scopus 로고    scopus 로고
    • A primer on Python for life science researchers
    • Bassi, S. (2007). A primer on Python for life science researchers. PLoS Comput. Biol. 3, e199.
    • (2007) PLoS Comput. Biol , vol.3
    • Bassi, S.1
  • 4
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • Bendtsen, J. D., Nielsen, H., von Heijne, G., and Brunak, S. (2004). Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795.
    • (2004) J. Mol. Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4
  • 5
    • 2442713832 scopus 로고    scopus 로고
    • GeneWise and genomewise
    • Birney, E., Clamp, M., and Durbin, R. (2004). GeneWise and genomewise. Genome Res. 14, 988-995.
    • (2004) Genome Res , vol.14 , pp. 988-995
    • Birney, E.1    Clamp, M.2    Durbin, R.3
  • 6
    • 43449126821 scopus 로고    scopus 로고
    • A neuropeptide-centric view of psychostimulant addiction
    • Boutrel, B. (2008). A neuropeptide-centric view of psychostimulant addiction. Br. J. Pharmacol. 154, 343-357.
    • (2008) Br. J. Pharmacol , vol.154 , pp. 343-357
    • Boutrel, B.1
  • 8
    • 30444432702 scopus 로고    scopus 로고
    • Neuropeptideprocessing enzymes: Applications for drug discovery
    • Fricker, L. D. (2005). Neuropeptideprocessing enzymes: applications for drug discovery. AAPS J. 7, E449-E455.
    • (2005) AAPS J , vol.7
    • Fricker, L.D.1
  • 9
    • 43449102252 scopus 로고    scopus 로고
    • Neuropeptides and social behavior: Effects of oxytocin and vasopressin in humans
    • Heinrichs, M., and Domes, G. (2008). Neuropeptides and social behavior: effects of oxytocin and vasopressin in humans. Prog. Brain Res. 170, 337-350.
    • (2008) Prog. Brain Res , vol.170 , pp. 337-350
    • Heinrichs, M.1    Domes, G.2
  • 10
    • 33750619248 scopus 로고    scopus 로고
    • Unique neuronal functions of cathepsin L and cathepsin B in secretory vesicles: Biosynthesis of peptides in neurotransmission and neurodegenerative disease
    • Hook, V. Y. (2006). Unique neuronal functions of cathepsin L and cathepsin B in secretory vesicles: biosynthesis of peptides in neurotransmission and neurodegenerative disease. Biol. Chem. 387, 1429-1439.
    • (2006) Biol. Chem , vol.387 , pp. 1429-1439
    • Hook, V.Y.1
  • 11
    • 41149103075 scopus 로고    scopus 로고
    • Proteases for processing proneuropeptides into peptide neurotransmitters and hormones
    • Hook, V., Funkelstein, L., Lu, D., Bark, S., Wegrzyn, J., and Hwang, S. (2008). Proteases for processing proneuropeptides into peptide neurotransmitters and hormones. Ann. Rev. Pharmac. Toxicol. 48, 393-423.
    • (2008) Ann. Rev. Pharmac. Toxicol , vol.48 , pp. 393-423
    • Hook, V.1    Funkelstein, L.2    Lu, D.3    Bark, S.4    Wegrzyn, J.5    Hwang, S.6
  • 12
    • 0346251363 scopus 로고    scopus 로고
    • From precursor to fi nal peptides: A statistical sequence-based approach to predicting prohormone processing
    • Hummon, A. B., Hummon, N. P., Corbin, R. W., Li, L. J., Vilim, F. S., Weiss, K. R., and Sweedler, J. V. (2003). From precursor to fi nal peptides: a statistical sequence-based approach to predicting prohormone processing. J. Proteome Res. 2, 650-656.
    • (2003) J. Proteome Res , vol.2 , pp. 650-656
    • Hummon, A.B.1    Hummon, N.P.2    Corbin, R.W.3    Li, L.J.4    Vilim, F.S.5    Weiss, K.R.6    Sweedler, J.V.7
  • 14
    • 74549143560 scopus 로고    scopus 로고
    • Sudbury, Massachusetts: Jones and Bartlett Publishers
    • Kinser, J. (2008). Python for Bioinformatics. Sudbury, Massachusetts: Jones and Bartlett Publishers.
    • (2008) Python For Bioinformatics
    • Kinser, J.1
  • 15
    • 51949104682 scopus 로고    scopus 로고
    • Peptides in the brain: Mass spectrometrybased measurement approaches and challenges
    • Li, L., and Sweedler, J. V. (2008). Peptides in the brain: mass spectrometrybased measurement approaches and challenges. Annu. Rev. Anal. Chem. 1, 451-483.
    • (2008) Annu. Rev. Anal. Chem , vol.1 , pp. 451-483
    • Li, L.1    Sweedler, J.V.2
  • 16
    • 0034623005 scopus 로고    scopus 로고
    • T-coffee: A novel method for multiple sequence alignments
    • Notredame, C., Higgins, D., and Heringa, J. (2000). T-coffee: a novel method for multiple sequence alignments. J. Mol. Biol. 302, 205-217.
    • (2000) J. Mol. Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.2    Heringa, J.3
  • 17
    • 34247500374 scopus 로고    scopus 로고
    • Python for scientifi c computing
    • Oliphant, T. E. (2007). Python for scientifi c computing. Comput. Sci. Eng. 9, 10-20.
    • (2007) Comput. Sci. Eng , vol.9 , pp. 10-20
    • Oliphant, T.E.1
  • 18
    • 34247352040 scopus 로고    scopus 로고
    • Evolutionary and biomedical insights from the rhesus macaque genome
    • Rhesus Macaque Genome Sequencing and Analysis Consortium
    • Rhesus Macaque Genome Sequencing and Analysis Consortium (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234.
    • (2007) Science , vol.316 , pp. 222-234
  • 19
    • 27144463192 scopus 로고    scopus 로고
    • On comparing classifi ers: Pitfals to avoid and a recommended approach
    • Salzberg, S. L. (1997). On comparing classifi ers: pitfals to avoid and a recommended approach. Data Min. Knowl. Disc. 1, 317-328.
    • (1997) Data Min. Knowl. Disc , vol.1 , pp. 317-328
    • Salzberg, S.L.1
  • 20
    • 33747866382 scopus 로고    scopus 로고
    • NeuroPred: A tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides
    • Southey, B. R., Amare, A., Zimmerman, T. A., Rodriguez-Zas, S. L., and Sweedler, J. V. (2006a). NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides. Nucleic Acids Res. 34, W267-W272.
    • (2006) Nucleic Acids Res , vol.34
    • Southey, B.R.1    Amare, A.2    Zimmerman, T.A.3    Rodriguez-Zas, S.L.4    Sweedler, J.V.5
  • 21
    • 33646144688 scopus 로고    scopus 로고
    • Prediction of neuropeptide prohormone cleavages with application to RFamides
    • Southey, B. R., Rodriguez-Zas, S. L., and Sweedler, J. V. (2006b) Prediction of neuropeptide prohormone cleavages with application to RFamides. Peptides 27, 1087-1098.
    • (2006) Peptides , vol.27 , pp. 1087-1098
    • Southey, B.R.1    Rodriguez-Zas, S.L.2    Sweedler, J.V.3
  • 22
    • 40749124939 scopus 로고    scopus 로고
    • Prediction of neuropeptide cleavage sites in insects
    • Southey, B. R., Sweedler, J. V., and Rodriguez-Zas, S. L. (2008). Prediction of neuropeptide cleavage sites in insects. Bioinformatics 24, 815-824.
    • (2008) Bioinformatics , vol.24 , pp. 815-824
    • Southey, B.R.1    Sweedler, J.V.2    Rodriguez-Zas, S.L.3
  • 23
    • 39149134576 scopus 로고    scopus 로고
    • Comparative analysis of neuropeptide cleavage sites in human, mouse, rat, and cattle
    • Tegge, A. N., Southey, B. R., Sweedler, J. V., and Rodriguez-Zas, S. L. (2008). Comparative analysis of neuropeptide cleavage sites in human, mouse, rat, and cattle. Mamm. Genome 19, 106-120.
    • (2008) Mamm. Genome , vol.19 , pp. 106-120
    • Tegge, A.N.1    Southey, B.R.2    Sweedler, J.V.3    Rodriguez-Zas, S.L.4
  • 24
    • 38549097071 scopus 로고    scopus 로고
    • The universal protein resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium (2008). The universal protein resource (UniProt). Nucleic Acids Res. 36, D190-D195.
    • (2008) Nucleic Acids Res , vol.36
  • 25
    • 84879282802 scopus 로고
    • The nucleotide sequence of cDNA coding for preproinsulin from the primate Macaca fascicularis
    • Wetekam, W., Groneberg, J., Leineweber, M., Wengenmayer, F., and Winnaker, E. -L. (1982). The nucleotide sequence of cDNA coding for preproinsulin from the primate Macaca fascicularis. Gene 19, 179-183.
    • (1982) Gene , vol.19 , pp. 179-183
    • Wetekam, W.1    Groneberg, J.2    Leineweber, M.3    Wengenmayer, F.4    Winnaker E., -L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.