Victor Wong
From OpenWetWare
Under Construction
Summer Intern
Victor is currently a student at The University of Pennsylvania who is interning in the Hoatlin lab during the summer of 2006. He enjoys table tennis, go cart racing, miniature golf and other miniaturized sports.
Building a Protein Model
Searching for Sequence Homologs
- Acquire sequence for the protein that you want to model (target sequence)
- Go to NCBI BLAST
- Click on position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)
- Enter your target sequence into the box labelled Search
- Change the database to "swissprot" in the Choose Database box
- Hit BLAST!
- Hit Format!
- Run PSI-BLAST iteration 3 or 4 times.
- Save sequences with high identity percentages
- Save as either a FASTA file or copy and paste each sequence into MacVector
Note: If you already know which homologs you are using and have the accession codes, it is possible to find the sequences at PubMed.
Aligning Homolog Sequences
MacVector
- Open all sequences
- Open Analyze and then click on ClustalW alignment
- Save Alignment as a FASTA file
ClustalW
- Paste all of your sequences into one FASTA file
- Select an online alignment program (CLUSTALW or TCoffee) depending on the number of sequences you are using and the total length of the sequences
- Upload your alignment
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