title: Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.
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.
authors.affiliation: Helix Research Institute, Yana, Kisarazu-shi, Chiba, Japan.
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Otsuki
authors.forename: Toshio
authors.initials: T
authors.lastname: Ota
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Nishikawa
authors.forename: Koji
authors.initials: K
authors.lastname: Hayashi
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Yamamoto
authors.forename: Ai
authors.initials: A
authors.lastname: Wakamatsu
authors.forename: Kouichi
authors.initials: K
authors.lastname: Kimura
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Sakamoto
authors.forename: Naoto
authors.initials: N
authors.lastname: Hatano
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kawai
authors.forename: Shizuko
authors.initials: S
authors.lastname: Ishii
authors.forename: Kaoru
authors.initials: K
authors.lastname: Saito
authors.forename: Shin-ichi
authors.initials: S
authors.lastname: Kojima
authors.forename: Tomoyasu
authors.initials: T
authors.lastname: Sugiyama
authors.forename: Tetsuyoshi
authors.initials: T
authors.lastname: Ono
authors.forename: Kazunori
authors.initials: K
authors.lastname: Okano
authors.forename: Yoko
authors.initials: Y
authors.lastname: Yoshikawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Aotsuka
authors.forename: Naokazu
authors.initials: N
authors.lastname: Sasaki
authors.forename: Atsushi
authors.initials: A
authors.lastname: Hattori
authors.forename: Koji
authors.initials: K
authors.lastname: Okumura
authors.forename: Keiichi
authors.initials: K
authors.lastname: Nagai
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Takao
authors.initials: T
authors.lastname: Isogai
mesh_terms: D024506:5' Flanking Region; D045744:Cell Line, Tumor; D003001:Cloning, Molecular; D015723:Gene Library; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics*; D009841:Oligonucleotides / Q000235:genetics; D021382:Protein Sorting Signals
chemical_list: D008565:Membrane Proteins; D009841:Oligonucleotides; D021382:Protein Sorting Signals