true or false. Polyhen 2 is a bioinformatics tool.
true
Polyhpen 2 was created by who?
researchers from Harvard Medical School, The max Planck Institute, the Russian Academy of Sciences, the University of Michigan, and the European Molecular Biology Laboratory
What does polyhen 2 predict?
The impact of point mutations on protein synthesis
Is polyphen 2 used casually or professionally?
both
What is the method for submitting proteins of interest?
You will have to specify the position of the mutation as well as the original amino acid (AA1) and the new amino acid causing the mutation (AA2)
What identifier is different than the rest?
SNP
What does the protein identifier do?
It recognizes protein accession numbers and entry names from Universal Protein Resource Knowledgebase or UniProtKB as well as RefSeq Identifiers and standard gene Symbols
How do you identify SNPs?
Same box as Protein Identifier. You will need the dbSNP reference ID for the protein
What is Protein sequence in FASTA format?
You will need to find a FASTA sequence for you protein either from NCBI or other database (UniProt is the one have used for far for our project). When you copy the FASTA sequence you need to highlight the definition line on top as well
The Query Description can be what?
It can be good to help you remember specific
information about
your gene or mutation, but it ultimately has no affect on your query submission
Why would the query description be good to use?
If you are submitting multiple queries as there is little to distinguish them from one another in your queue
What is the grid gateway interference page?
the page where all your submitted queries are listed and queued up
Your grid status can be an indicator of what?
Of how quickly you will be able to get results
Every report contains how many analyzing information sections?
3
What does the query section contain?
<p>Displays the protein information submitted during the query. Provides additional context about the protein on the right side.</p> <br>
What does the results section contain?
Presents variant effect prediction scores ranging from 0 to 1. Labels variants as benign, possibly damaging, or probably damaging, with accompanying sensitivity and specificity scores to indicate prediction confidence.
What does the details section contain?
<p>Features a multiple sequence alignment showing 75 amino acids around the variant, including similar proteins from other species. Links to UniProt for more information on protein effects in other species. May include an associated 3D structure from the Protein Data Bank, though availability varies by protein and variant.</p> <br>
olyPhen-2 will not provide a prediction score and will report the HumDiv and HumVar results as what?
unknown
PolyPhen-2 divides all variant effect prediction scores into what three categories?
benign, possibly damaging, and probably damaging
A result of benign indicates what?
That the variant is not likely to affect protein function.
The result of possibly damaging indicates what?
That the variant may affect protein function.
A result of probably damaging indicates what?
That the variant is likely to affect protein function.
What did the TAS2R38 variant predict?
Both models predicted that the variant is possibly damaging
What is the full name for polyphen 2?
Polymorphism phenotyping v2
read paper on polyphen 2
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