Menu ▾ ▴

#133 QC: check allele descriptions match current gene sequence (possible student project)

next-load
open
nobody
None
1
2013-09-10
2012-11-12
Valerie Wood
No

Gene structures are sometimes updated which may make some allele descriptions incorrect. Luckily this won't usually happen because if a gene structure is wrong it is usually an uncharacterised gene, not one which has been studied in depth. However we need to be aware of this. At some point in the future, maybe we can get a student to make a program to alert us when the allele residues do not match the protein. I guess this will happen any way if we try to do anything with these down the line....

Discussion

  • Valerie Wood

    Valerie Wood - 2013-09-03
    • summary: potential for problems with allele descriptios --> potential for problems with allele descriptions (possible student project)
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1,2 +1 @@
-
-Gene structures are sometimes updated which may make some allele descriptions incorrect. Luckily this won't usually happen becase if a gene structure is wrong it is usually an uncharacterised gene, not one which has been studied in depth. However we need to be aware of this. At some point in the future, maybe we can get a student to make a program to alert us when the allele residues do not match  the protein. I guess this will happen any way if we try to do anything with these down the line....
+Gene structures are sometimes updated which may make some allele descriptions incorrect. Luckily this won't usually happen because if a gene structure is wrong it is usually an uncharacterised gene, not one which has been studied in depth. However we need to be aware of this. At some point in the future, maybe we can get a student to make a program to alert us when the allele residues do not match  the protein. I guess this will happen any way if we try to do anything with these down the line....
    • Group: --> next-load
     

  • Valerie Wood

    Valerie Wood - 2013-09-03

    (transferred from duplicate
    https://sourceforge.net/p/pombase/chado/224/

    (Transferred from [curation-tool:#451])

    check for example that if the description is "A22F" that amino acid 22 really is an "A", (because sometimes sequence coordinates will have changed since alleles were published)

    we could do something with implementing checks like this as part of a student task maybe?….
    Related

    Ticket: #451

     

    Related

    Curation tool: #451

  • Valerie Wood

    Valerie Wood - 2013-09-10
    • summary: potential for problems with allele descriptions (possible student project) --> QC: check allele descriptions match current gene sequence (possible student project)
     

Log in to post a comment.