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Published 20 hours ago • verified publisher icon milaboratory

Align D gene even when V or J is absent

Open PoslavskySV opened this issue 7 years ago • 4 comments

PoslavskySV avatar Feb 20 '17 16:02 PoslavskySV

@mikessh

dbolotin avatar Feb 20 '17 16:02 dbolotin

Actually the full list of what is needed (i.e. observed in lymphoma samples):

  • Vd-Dd3, Dd2-Jd
  • Dd-Ja
  • Dh-Jh
  • More complex: Dd2-Dd3, Vk-KDE, INTRON-KDE (IGK)

here d,a,h,k stands for TRD,TRA,IGH,IGK

mikessh avatar Feb 20 '17 17:02 mikessh

To speed up it is reasonable to suggest that best D match cannot be more than 30 bases from the available reference point

mikessh avatar Feb 20 '17 17:02 mikessh

Requires additional threshold in parameters for minimal score for incomplete alignments. Floating bounds ? Once again, is it possible to add several separate D gene hits into our abstraction? Stas?

dbolotin avatar Feb 28 '17 21:02 dbolotin