![]() In addition, the entries in SPD were not checked manually against the publications. TrEMBL is generated from an automated pipeline and has yet to undergo manual curation. SPD aims to be a comprehensive repository for secreted proteins, but it suffers from providing datasets that may still contain many erroneous annotations from its underlying data sources for example TrEMBL. It also includes datasets from the Secreted Protein Discovery Initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins the Riken mouse secretome and seven other related datasets. SPD or secreted protein database is a collection of proteins from the human, mouse and rat proteomes originating from databases such as TrEMBL, Ensembl and Refseq. ![]() These databases do not provide signal peptide specific information except for SPD. Searching through popular search engines and reviewing the Nucleic Acids Research database list reveal several databases that provide information on protein subcellular localisation, nuclear proteins and secreted proteins. This repetitive process can and should be eliminated by creating a centralised repository of signal peptide sequences. As a preparatory step for prediction work, researchers often devote considerable time sifting through primary databases such as Swiss-Prot, EMBL and other databases to collate and construct their own datasets. These prediction tools require training and testing datasets. Over the years, several prediction tools have been developed to predict the cleavage sites of signal peptides. Interestingly, not all proteins possess signal peptides, suggesting that other mechanisms for protein targeting exist. The signal peptides are cleaved off and degraded upon reaching their targeted locations. They function like a postal address label on an envelope by targeting the proteins for secretion or to specific organelle for further processing. Signal peptides are present in both prokaryotic and eukaryotic cells, indicating its ancient universal origins. One of the commonly occurring signals is formed by short, transient peptides known as signal peptides or leader sequences, which are usually found at the amino terminus of secreted proteins. There are many different classes of targeting signals. This process is known as protein targeting and it depends on targeting signals to direct the proteins to their specific locations. Proteins synthesised at the ribosome (cytoplasm or rough endoplasmic reticulum), mitochondria or chloroplast are transported to their site of function. Günter Blobel discovered that "proteins have intrinsic signals that govern their transport and localization in the cell". SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date. SPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. 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. The database update is semi-automated with human checking and verification of the data to ensure the correctness of the data stored. SPdb integrates information from two sources (a) Swiss-Prot protein sequence database which is now part of UniProt and (b) EMBL nucleotide sequence database. To support this understanding, we present SPdb signal peptide database, a repository of experimentally determined and computationally predicted signal peptides. Understanding how signal peptides function is crucial in predicting where proteins are translocated. 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. The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells.
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