Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries - PubMed (original) (raw)

doi: 10.1093/dnares/12.2.117.

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, Takao Isogai

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• PMID: 16303743
• DOI: 10.1093/dnares/12.2.117

Free article

Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries

Tetsuji Otsuki et al. DNA Res. 2005.

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Abstract

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.

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