| URL: | http://ms3d.jp/software/proteincarta |
| Full name: | Protein Catalog indexed by Recorded Terminal Tags |
| Description: | ProteinCarta is a terminal tag sequence database which includes all terminal tags of proteomes from the nine organisms analyzed, in order to confirm the specificity of terminal tags and to identify the parent protein. We hope that ProteinCarta will contribute to the identification of proteins and/or unrevealed signal peptides or propeptides and further analyses. |
| Year founded: | 2015 |
| Last update: | |
| Version: | 0.10 |
| Accessibility: |
Accessible
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| Country/Region: | Japan |
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| University/Institution: | Shimadzu Corporation |
| Address: | Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, Kyoto 604-8511, Japan |
| City: | Kyoto |
| Province/State: | |
| Country/Region: | Japan |
| Contact name (PI/Team): | Akiyasu C. Yoshizawa |
| Contact email (PI/Helpdesk): | acyshzw@shimadzu.co.jp |
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Computational survey of sequence specificity for protein terminal tags covering nine organisms and its application to protein identification. [PMID: 25393771]
In 1998, Wilkins et al. (J. Mol. Biol. 1998, 278, 599-608) reported high specificity in terminal regions (terminal tags) of 15?519 proteins from five organisms and proposed a methodology for identifying proteins by terminal tags. However, their examined sequence data were not based on complete genome sequences. Here, we examined current proteome data (217?249 entries from UniProt 2013_6 complete/reference proteome for nine organisms including human) in terms of the specificity of terminal tags and their computational annotation. One example from the results indicated that the specificity of N-terminal tags plateaued at 28% at a length of six residues for human; even when using both N- and C-terminal tags, specificity was merely 66%. In order to determine the cause of these low specificities, the annotation of proteins sharing terminal tags with other proteins was examined. The results suggested that a large majority were phylogenetically or functionally related, whereas nonrelated proteins sharing terminal tags made up less than 1% of human proteome data. On the basis of these findings, we constructed the terminal tag sequence database ProteinCarta (http://ms3d.jp/software/proteincarta/), which includes all terminal tags of proteomes from the nine organisms analyzed here, in order to confirm the specificity of terminal tags and to identify the parent protein. |