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

• Published in: DNA research Vol. 12; no. 2; pp. 117 - 126
• Main Authors: Otsuki, Tetsuji, Ota, Toshio, Nishikawa, Tetsuo, Hayashi, Koji, Suzuki, Yutaka, Yamamoto, Jun-ichi, Wakamatsu, Ai, Kimura, Kouichi, Sakamoto, Katsuhiko, Hatano, Naoto, Kawai, Yuri, Ishii, Shizuko, Saito, Kaoru, Kojima, Shin-ichi, Sugiyama, Tomoyasu, Ono, Tetsuyoshi, Okano, Kazunori, Yoshikawa, Yoko, Aotsuka, Satoshi, Sasaki, Naokazu, Hattori, Atsushi, Okumura, Koji, Nagai, Keiichi, Sugano, Sumio, Isogai, Takao
• Format: Journal Article
• Language: English
• Published: England 2005
• Subjects: 5' Flanking Region; Cell Line, Tumor; Cloning, Molecular; Gene Library; Humans; Membrane Proteins - genetics; Oligonucleotides - genetics; Protein Sorting Signals
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/12.2.117

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.