Angela A. Garibaldi Week 8: Difference between revisions
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(→Retrieving a List of Related Protein Sequences: add reading Swiss-Prot Entry) |
(→Reading a Swiss-Prot Entry: mid ORF) |
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'''Entry Name: ENV_HV1H2''' | '''Entry Name: ENV_HV1H2''' | ||
'''Accession Number: P04578''' | '''Accession Number: P04578''' | ||
*Scroll down to '''Sequence Annotation - Region''' to Look at V3 sequence specifically. | |||
==ORFing your DNA Sequences== | |||
#Go to [[www.ncbi.nlm.nih.gov/gorf/gorf.html NCBI ORF Finder]] | |||
#Input a DNA sequence for practice |
Revision as of 12:59, 9 March 2010
Retrieving Protein Sequences
- Go to UniProt www.expasy.org/sprot UniProt
- Enter dUTPase in search window. This produces more than 3 relevant sequences, so found DUT ECOLI (P06968) on page 4
- Scroll down for FASTA format of amino acid sequences
- In the case that your beginning information is not enough to find the protein sequence you seek,
- find the advanced search option. This no longer exists. You have to click the add and search button and a drop down menu will be displayed to give you the same search options as described in Figure 2-16 of the Bioinformatics for Dummeies
Retrieving a List of Related Protein Sequences
- Go to the Advanced Search UniProt as described above
- Because the advanced search is completely different, cannot deselect TrEMBL. Instead Select Reviewed- Yes as an alternative
- Input dUTPase in search again. There is no "description" field any longer.Yields many possibilities
- Since there are more than 211 total possibilities, so we selected entire first page of sequences (25)
- In newer version click retrieve at the bottom right corner instead of french button.
- Once you retrieve these, it is put into a list of which you can add to and then below choose the format you want the sequences in. No longer have to copy and paste into a document. FASTA format is available.
Reading a Swiss-Prot Entry
This time we skipped the example and did the activity using HIV gp120.
- Select the Reviewed - Yes. Our overall query to achieve these results: HIV gp120 AND reviewed:yes
- We selected the first option in the list
Entry Name: ENV_HV1H2 Accession Number: P04578
- Scroll down to Sequence Annotation - Region to Look at V3 sequence specifically.
ORFing your DNA Sequences
- Go to www.ncbi.nlm.nih.gov/gorf/gorf.html NCBI ORF Finder
- Input a DNA sequence for practice