Academic Journal
Quantitative assessment of protein function prediction from metagenomics shotgun sequences
| العنوان: | Quantitative assessment of protein function prediction from metagenomics shotgun sequences |
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| المؤلفون: | Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J., Bork, P. |
| بيانات النشر: | National Academy of Sciences |
| سنة النشر: | 2007 |
| المجموعة: | Max-Delbrueck-Center for Molecular Medicine, Berlin: MDC Repository |
| مصطلحات موضوعية: | Cardiovascular and Metabolic Diseases |
| الوصف: | To assess the potential of protein function prediction in environmental genomics data, we analyzed shotgun sequences from four diverse and complex habitats. Using homology searches as well as customized gene neighborhood methods that incorporate intergenic and evolutionary distances, we inferred specific functions for 76% of the 1.4 million predicted ORFs in these samples (83% when nonspecific functions are considered). Surprisingly, these fractions are only slightly smaller than the corresponding ones in completely sequenced genomes (83% and 86%, respectively, by using the same methodology) and considerably higher than previously thought. For as many as 75,448 ORFs (5% of the total), only neighborhood methods can assign functions, illustrated here by a previously undescribed gene associated with the well characterized heme biosynthesis operon and a potential transcription factor that might regulate a coupling between fatty acid biosynthesis and degradation. Our results further suggest that, although functions can be inferred for most proteins on earth, many functions remain to be discovered in numerous small, rare protein families. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | unknown |
| Relation: | Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Harrington, E.D. and Singh, A.H. and Doerks, T. and Letunic, I. and von Mering, C. and Jensen, L.J. and Raes, J. and Bork, P. Proceedings of the National Academy of Sciences of the United States of America 104 (35): 13913-13918. 28 August 2007 |
| DOI: | 10.1073/pnas.0702636104 |
| الاتاحة: | http://edoc.mdc-berlin.de/8912/ https://edoc.mdc-berlin.de/8912/ https://doi.org/10.1073/pnas.0702636104 |
| رقم الانضمام: | edsbas.78029502 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1073/pnas.0702636104 |
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