+
Skip to content

feature based reverse engineering #32

Open
@jjti

Description

@jjti
  • 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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions

      点击 这是indexloc提供的php浏览器服务,不要输入任何密码和下载