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Pripper: prediction of caspase cleavage sites from whole proteomes
- Source :
- BMC Bioinformatics, BMC Bioinformatics, Vol 11, Iss 1, p 320 (2010)
- Publication Year :
- 2010
-
Abstract
- Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s) and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for reading an arbitrary number of proteins in FASTA format, predicting their caspase cleavage sites and outputting the cleaved sequences to a new FASTA format sequence file. We show that Pripper is a valuable tool in identifying novel caspase target proteins from modern proteomics experiments.
- Subjects :
- Proteomics
Proteome
PROTEINS
0206 medical engineering
Caspase 2
education
Caspase 3
02 engineering and technology
Computational biology
lcsh:Computer applications to medicine. Medical informatics
Caspase 7
Biochemistry
03 medical and health sciences
Structural Biology
Sequence Analysis, Protein
Databases, Protein
lcsh:QH301-705.5
Molecular Biology
Caspase
030304 developmental biology
0303 health sciences
biology
NLRP1
Applied Mathematics
FASTA format
Cell biology
Computer Science Applications
APOPTOSIS
NETWORKS
FAMILY
MODEL
lcsh:Biology (General)
Caspases
biology.protein
lcsh:R858-859.7
Caspase 10
118 Biological sciences
020602 bioinformatics
Software
Subjects
Details
- ISSN :
- 14712105
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- BMC bioinformatics
- Accession number :
- edsair.doi.dedup.....67f547b71c14a57c1f367e6cc7351c2a