AninditaVarshneya BIOL368 Week 9: Difference between revisions
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===Purpose=== | ===Purpose=== | ||
===Methods and Results=== | ===Methods and Results=== | ||
* Convert DNA sequence of subject 4 during visit one into a protein sequence using [https://www.ncbi.nlm.nih.gov/orffinder/ NCBI ORF Finder] | |||
** The frame without the stop codon is the true open reading frame. | |||
** My translated protein sequence: E V V I R S E N F T N N A K I I I V Q L N E S V E I N C T R P N N N T R K S I H I G P G R A F Y T T G D I I G D I R Q A Y C N I S R A E W N N T L K H I V I K L R E H F G N K T I V F N H S S | |||
** Markham et al. protein sequence: EVVIRSENFTNNAKIIIVQLNKSVEINCTRPNNNTIRRIPIGPGRAFYTTGRIGDIRPAHCNISRTKWNNALKLIVNKLREQFRNKTIIFNQSS | |||
* Learn more the gp120 protein using [http://www.uniprot.org/ UniProt Knowledgebase (UniProt KB)] | |||
** Searching "HIV gp120" returned 206,278 results | |||
** I selected the entry with the accession number: P04578 | |||
** The types of information provided include: | |||
*** Function, Names and Taxonomy, Subcellular location, Pathology/Biotechnology, PTM/Processing, Interaction, Structure, Family and Domains, Sequence, Cross-references, Entry information, Similar proteins, and other miscellaneous information. | |||
* Use the [https://ppopen.informatik.tu-muenchen.de/ Predict Protein Server] to analyze the V3 region of Subject 4, Visit 1-1 | |||
** Copy and paste their sequence from the [http://bioquest.org/bedrock/problem_spaces/hiv/amino_acid_sequences.php Bedrock HIV Problem Space] into PPS | |||
===Conclusion=== | ===Conclusion=== | ||
===Data and Files=== | ===Data and Files=== | ||
==Defining the Research Project== | ==Defining the Research Project== | ||
==Acknowledgements== | ==Acknowledgements== | ||
Revision as of 16:29, 25 October 2016
Electronic Lab Notebook
Purpose
Methods and Results
- Convert DNA sequence of subject 4 during visit one into a protein sequence using NCBI ORF Finder
- The frame without the stop codon is the true open reading frame.
- My translated protein sequence: E V V I R S E N F T N N A K I I I V Q L N E S V E I N C T R P N N N T R K S I H I G P G R A F Y T T G D I I G D I R Q A Y C N I S R A E W N N T L K H I V I K L R E H F G N K T I V F N H S S
- Markham et al. protein sequence: EVVIRSENFTNNAKIIIVQLNKSVEINCTRPNNNTIRRIPIGPGRAFYTTGRIGDIRPAHCNISRTKWNNALKLIVNKLREQFRNKTIIFNQSS
- Learn more the gp120 protein using UniProt Knowledgebase (UniProt KB)
- Searching "HIV gp120" returned 206,278 results
- I selected the entry with the accession number: P04578
- The types of information provided include:
- Function, Names and Taxonomy, Subcellular location, Pathology/Biotechnology, PTM/Processing, Interaction, Structure, Family and Domains, Sequence, Cross-references, Entry information, Similar proteins, and other miscellaneous information.
- Use the Predict Protein Server to analyze the V3 region of Subject 4, Visit 1-1
- Copy and paste their sequence from the Bedrock HIV Problem Space into PPS
Conclusion
Data and Files
Defining the Research Project
Acknowledgements
References
Other Links
User Page: Anindita Varshneya
Bioinfomatics Lab: Fall 2016
Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016
| Weekly Assignments | Individual Journal Assignments | Shared Journal Assignments |
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SURP 2015
Links: Electronic Lab Notebook
