SPdb – a signal peptide database

<p>Abstract</p> <p>Background</p> <p>The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting pr...

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Main Authors: Tan Tin, Choo Khar, Ranganathan Shoba
Format: Article
Language:English
Published: BMC 2005-10-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/6/249
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spelling doaj-583327b3af05485d9447278d6d5ca6832020-11-24T23:07:49ZengBMCBMC Bioinformatics1471-21052005-10-016124910.1186/1471-2105-6-249SPdb – a signal peptide databaseTan TinChoo KharRanganathan Shoba<p>Abstract</p> <p>Background</p> <p>The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Understanding how signal peptides function is crucial in predicting where proteins are translocated. To support this understanding, we present SPdb signal peptide database <url>http://proline.bic.nus.edu.sg/spdb</url>, a repository of experimentally determined and computationally predicted signal peptides.</p> <p>Results</p> <p>SPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146 entries of which 2,584 entries are experimentally verified signal sequences; the remaining 15,562 entries are either signal sequences that fail to meet our filtering criteria or entries that contain unverified signal sequences.</p> <p>Conclusion</p> <p>SPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date.</p> http://www.biomedcentral.com/1471-2105/6/249
collection DOAJ
language English
format Article
sources DOAJ
author Tan Tin
Choo Khar
Ranganathan Shoba
spellingShingle Tan Tin
Choo Khar
Ranganathan Shoba
SPdb – a signal peptide database
BMC Bioinformatics
author_facet Tan Tin
Choo Khar
Ranganathan Shoba
author_sort Tan Tin
title SPdb – a signal peptide database
title_short SPdb – a signal peptide database
title_full SPdb – a signal peptide database
title_fullStr SPdb – a signal peptide database
title_full_unstemmed SPdb – a signal peptide database
title_sort spdb – a signal peptide database
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2005-10-01
description <p>Abstract</p> <p>Background</p> <p>The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further processing. Understanding how signal peptides function is crucial in predicting where proteins are translocated. To support this understanding, we present SPdb signal peptide database <url>http://proline.bic.nus.edu.sg/spdb</url>, a repository of experimentally determined and computationally predicted signal peptides.</p> <p>Results</p> <p>SPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. The latest release SPdb release 3.2 contains 18,146 entries of which 2,584 entries are experimentally verified signal sequences; the remaining 15,562 entries are either signal sequences that fail to meet our filtering criteria or entries that contain unverified signal sequences.</p> <p>Conclusion</p> <p>SPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date.</p>
url http://www.biomedcentral.com/1471-2105/6/249
work_keys_str_mv AT tantin spdbasignalpeptidedatabase
AT chookhar spdbasignalpeptidedatabase
AT ranganathanshoba spdbasignalpeptidedatabase
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