BIOL368/F14:Chloe Jones Week 8
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Working with Protein Sequences In-class Activity
Chapter 4: Reading a SWISS-PROT entry
Source: Bioinformatics for Dummies pp.110-123
- Using the database UniProt KB which has two subsections: Swis-Prot and TrEMBL.
- If you search on the keywords "HIV" and "gp120", how many results do you get?
- 180,227 results.
General Information about the entry
- Entry name: 9HIV1
- Primary Accession Number :Q75760
- Secondary Accession Numbers :N/A
- Intergrated into Swiss-Prot on :November 1, 1996
- Sequence was last modified on : November 1, 1996
- Annotations were last modified on : October 1, 2014
Name and origin of the protein
- Protein name:Envelope glycoprotein gp160
- Synonyms:N/A
- Gene name:Env
- From:Homo sapiens (Human) [TaxID: 9606] TaxID:9606
- Taxonomy: Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group
References
- Number of references:9
The comments :?? The cross references :172
- ENA, European Nucleotide Archive (more information possibly)
Keyword
- Apoptosis, fushion of virus membrane with host membrane, host-virus interaction, viral attachment to host cell, viral immunoevasion, Viral penetration into host cytoplasm, virus entry into host cell
Chapter 5: ORFing your DNA sequence
Source: Bioinformatics for Dummies pp.146-147
- Fasta format of Envelope glycoprotein gp160 obtained from UniProt KB was placed in the in the imput box of ORF Finder(Open Reading Frame Finder). 6 parallel horizontal bars were present with integers correlating to the reading frame.
- Putting in DNA sequences: Subject 1 visit 1, clone 1:
- The protein with the open reading frame was in the ORF Finder database was projected to be #2, or #3. Looking at the exPASy database 5’3” Frame 3 had an open reading frame with no stop codons interrupting /truncating the lengh of the DNA.
- Apoptosis, fushion of virus membrane with host membrane, host-virus interaction, viral attachment to host cell, viral immunoevasion, Viral penetration into host cytoplasm, virus entry into host cell
The features Media***
Chapter 6:Working with a single protein sequence
Source: Bioinformatics for Dummies pp.159-195
