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| Status |
Public on Apr 23, 2021 |
| Title |
Estimation of peptide elongation times from ribosome profiling spectra |
| Organism |
Escherichia coli |
| Experiment type |
Other
|
| Summary |
We develop a model for ribosome-protected fragment (RPF) spectra that accounts for the local codon context-dependent variation of peptide elongation times and fragment processing biases. We use a Marquardt algorithm for non-linear regression with maximum likelihood (ML) like statistics to fit the RPF sequencing data. Taking advantage of the factorial character of the present model, we reconstruct the parameters adhering to an ideal, unbiased RPF spectrum.
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| Overall design |
Ribosome profiling of E. coli MG1655 cultured in rich medium
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| Web link |
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab260/6246399?guestAccessKey=d3b4bb4e-f84e-4c09-8734-d9bae3dc91c1
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| Contributor(s) |
Pavlov M, Ullman G, Ignatova Z, Eherenberg M |
| Citation(s) |
33885812 |
| Submission date |
Feb 19, 2020 |
| Last update date |
Apr 25, 2021 |
| Contact name |
Zoya Ignatova |
| E-mail(s) |
zoya.ignatova@chemie.uni-hamburg.de
|
| Organization name |
Universitaet Hamburg
|
| Street address |
Martin -Luther-King-Platz 6
|
| City |
Hamburg |
| ZIP/Postal code |
20146 |
| Country |
Germany |
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| Platforms (1) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA607566 |
| SRA |
SRP250036 |
