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The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. Overbeek R, et al. Among authors: ye y. Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. doi: 10.1093/nar/gki866. Print 2005. Nucleic Acids Res. 2005. PMID: 16214803 Free PMC article.
The amphioxus genome illuminates vertebrate origins and cephalochordate biology.
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. Holland LZ, et al. Among authors: ye y. Genome Res. 2008 Jul;18(7):1100-11. doi: 10.1101/gr.073676.107. Epub 2008 Jun 18. Genome Res. 2008. PMID: 18562680 Free PMC article.
POSA: a user-driven, interactive multiple protein structure alignment server.
Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. Li Z, et al. Among authors: ye y. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W240-5. doi: 10.1093/nar/gku394. Epub 2014 May 16. Nucleic Acids Res. 2014. PMID: 24838569 Free PMC article.
POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. ...
POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment intro …
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