front 1 true or false. Polyhen 2 is a bioinformatics tool. | back 1 true |
front 2 Polyhpen 2 was created by who? | back 2 researchers from Harvard Medical School, The max Planck Institute, the Russian Academy of Sciences, the University of Michigan, and the European Molecular Biology Laboratory |
front 3 What does polyhen 2 predict? | back 3 The impact of point mutations on protein synthesis |
front 4 Is polyphen 2 used casually or professionally? | back 4 both |
front 5 What is the method for submitting proteins of interest? | back 5 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) |
front 6 What identifier is different than the rest? | back 6 SNP |
front 7 What does the protein identifier do? | back 7 It recognizes protein accession numbers and entry names from Universal Protein Resource Knowledgebase or UniProtKB as well as RefSeq Identifiers and standard gene Symbols |
front 8 How do you identify SNPs? | back 8 Same box as Protein Identifier. You will need the dbSNP reference ID for the protein |
front 9 What is Protein sequence in FASTA format? | back 9 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 |
front 10 The Query Description can be what? | back 10 It can be good to help you remember specific |
front 11 Why would the query description be good to use? | back 11 If you are submitting multiple queries as there is little to distinguish them from one another in your queue |
front 12 What is the grid gateway interference page? | back 12 the page where all your submitted queries are listed and queued up |
front 13 Your grid status can be an indicator of what? | back 13 Of how quickly you will be able to get results |
front 14 Every report contains how many analyzing information sections? | back 14 3 |
front 15 What does the query section contain? | back 15 <p>Displays the protein information submitted during the query. Provides additional context about the protein on the right side.</p> <br> |
front 16 What does the results section contain? | back 16 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. |
front 17 What does the details section contain? | back 17 <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> |
front 18 olyPhen-2 will not provide a prediction score and will report the HumDiv and HumVar results as what? | back 18 unknown |
front 19 PolyPhen-2 divides all variant effect prediction scores into what three categories? | back 19 benign, possibly damaging, and probably damaging |
front 20 A result of benign indicates what? | back 20 That the variant is not likely to affect protein function. |
front 21 The result of possibly damaging indicates what? | back 21 That the variant may affect protein function. |
front 22 A result of probably damaging indicates what? | back 22 That the variant is likely to affect protein function. |
front 23 What did the TAS2R38 variant predict? | back 23 Both models predicted that the variant is possibly damaging |
front 24 What is the full name for polyphen 2? | back 24 Polymorphism phenotyping v2 |
front 25 read paper on polyphen 2 | back 25 kkkk |