Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.
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.
Otsuki
Tetsuji
T
Helix Research Institute, Yana, Kisarazu-shi, Chiba, Japan.
Ota
Toshio
T
Nishikawa
Tetsuo
T
Hayashi
Koji
K
Suzuki
Yutaka
Y
Yamamoto
Jun-ichi
J
Wakamatsu
Ai
A
Kimura
Kouichi
K
Sakamoto
Katsuhiko
K
Hatano
Naoto
N
Kawai
Yuri
Y
Ishii
Shizuko
S
Saito
Kaoru
K
Kojima
Shin-ichi
S
Sugiyama
Tomoyasu
T
Ono
Tetsuyoshi
T
Okano
Kazunori
K
Yoshikawa
Yoko
Y
Aotsuka
Satoshi
S
Sasaki
Naokazu
N
Hattori
Atsushi
A
Okumura
Koji
K
Nagai
Keiichi
K
Sugano
Sumio
S
Isogai
Takao
T
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
D008565:Membrane Proteins; D009841:Oligonucleotides; D021382:Protein Sorting Signals