I have a table of blast hits in a database that I'd like to chain. What is a good choice for a 'stand alone' chaining tool? Is it simple to implement in Perl, for example?

Example 'hit' data is here. Background is here

  • $\begingroup$ Do you know any existing stand alone chaining tools? How do you define good choice (fast, accurate, easy,..)? You have the description of the algorithm on page 19. And some implementations linked on page 38. $\endgroup$ – llrs Aug 18 '18 at 11:02
  • $\begingroup$ Ideally I'd like something I can understand in a short subroutine. $\endgroup$ – Dan Aug 20 '18 at 14:21
  • $\begingroup$ What is short? I find the question unclear to search for solutions or to build such short "subroutine". $\endgroup$ – llrs Aug 20 '18 at 15:08
  • $\begingroup$ I'm not able to implement the algorithm on page 19. I'm looking for an implementation of that algorithm in Perl or Python that I can feed my hits to. $\endgroup$ – Dan Aug 21 '18 at 10:14
  • $\begingroup$ it is easier to get help how to correctly implement an algorithm than get an algorithm implemented for you. If you could post your code and your problems in the question someone could help you to implement it. How wasn't the implementations on page 38 not helpful? $\endgroup$ – llrs Aug 21 '18 at 10:39

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