Journal Article

Signal Sequence and Keyword Trap <i>in silico</i> for Selection of Full-Length Human cDNAs Encoding Secretion or Membrane Proteins from Oligo-Capped cDNA Libraries

Tetsuji Otsuki, Toshio Ota, Tetsuo Nishikawa, Koji Hayashi, Yutaka Suzuki, Jun-ichi Yamamoto, Ai Wakamatsu, Kouichi Kimura, Katsuhiko Sakamoto, Naoto Hatano, Yuri Kawai, Shizuko Ishii, Kaoru Saito, Shin-ichi Kojima, Tomoyasu Sugiyama, Tetsuyoshi Ono, Kazunori Okano, Yoko Yoshikawa, Satoshi Aotsuka, Naokazu Sasaki, Atsushi Hattori, Koji Okumura, Keiichi Nagai, Sumio Sugano and Takao Isogai

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 12, issue 2, pages 117-126
Published in print January 2005 | ISSN: 1340-2838
Published online January 2005 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/12.2.117

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We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5′-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT (‘signal sequence trap’). We also applied ‘secretion or membrane protein-related keyword trap’ based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by ‘keyword trap’ preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.

Keywords: oligo-capping; human full-length cDNA; mRNA; secretion protein; membrane protein

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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