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feature based reverse engineering #32

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7 of 10 tasks
jjti opened this issue Feb 2, 2019 · 0 comments
Open
7 of 10 tasks

feature based reverse engineering #32

jjti opened this issue Feb 2, 2019 · 0 comments

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@jjti
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jjti commented Feb 2, 2019

  • blast each feature against the databases, store in a map from feature name to a list of matches with that feature
  • traverse the ordered list of features and find the minimum cost/length combinations of fragments/vectors to assemble a vector with all the features in order (returning all solutions)
  • add dbs flag to 'defrag features find' allow checking of features in databases as well will add 'defrag ls fragment [name]' instead
  • return pareto optimal solutions

Feature CLI Grammar

[name]:fwd/rev:l#:r#

  • fwd/rev = whether it's in fwd or rev direction, fwd assumed
  • l# = upper bound on "padding" in bp to consume from the left matched fragment
  • r# = upper bound on "padding" in bp to consume from the right matched fragment

default l/r is unlimited for matches that contain adjacent features and 0 for matches without any other additional features

Longterm

  • read in Genbank file features and use
  • read in multi-FASTA file features
  • gap penalty for inserting a new feature? Post assembly, blast each vector solution against the features db and penalize those that added new features
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