Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/5047
Title: De novo markup language, a standard to represent de novo sequencing results from MS/MS data
Authors: Takan, Savaş
Allmer, Jens
Takan, Savaş
Allmer, Jens
Izmir Institute of Technology. Computer Engineering
Keywords: Database searches
De novo sequencing
Learning curves
Proteins
Proteomics
Issue Date: 2012
Publisher: Institute of Electrical and Electronics Engineers Inc.
Source: Takan, S., and Allmer, J. (2012, April 19-22). De novo markup language, a standard to represent de novo sequencing results from MS/MS data. Paper presented at the 7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012. doi:10.1109/HIBIT.2012.6209038
Abstract: Proteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins, mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics, proteins can be identified or sequenced by either database search or de novo sequencing. Both methods have certain advantages and drawbacks but in the long run we envision de novo sequencing to become the predominant tool. Currently, de novo sequencing results are stored in arbitrary file formats, depending on the developers of the algorithms. We identified this as a large and unnecessary obstacle while integrating results from multiple de novo sequencing algorithms. Therefore, we designed a standard file format for the representation of de novo sequencing results. We further developed an application programming interface since we identified the lack of proper APIs as another obstacle, introducing a needlessly high learning curve for developers. © 2012 IEEE.
Description: 7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012; Cappadocia; Turkey; 19 April 2012 through 22 April 2012
URI: http://doi.org/10.1109/HIBIT.2012.6209038
http://hdl.handle.net/11147/5047
ISBN: 9781467308786
Appears in Collections:Computer Engineering / Bilgisayar Mühendisliği
Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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