<p>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?</p>

<p>Example 'hit' data is <a href="https://gist.githubusercontent.com/dbolser/c0e9d570b7023997ca6488bc483d208c/raw/1afc051d356409d8521ff35be086ce6cc8ed27f2/dummy%2520data.txt" rel="nofollow noreferrer">here</a>. Background is <a href="http://www.mi.fu-berlin.de/wiki/pub/ABI/GenomeComparisonP4/chaining.pdf" rel="nofollow noreferrer">here</a></p>

CC BY-SA 4.0
2018-08-18T11:02:56.213Z
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.
llrs
CC BY-SA 4.0
2018-08-20T14:21:37.617Z
Ideally I'd like something I can understand in a short subroutine.
Dan
CC BY-SA 4.0
2018-08-20T15:08:39.147Z
What is short? I find the question unclear to search for solutions or to build such short "subroutine".
llrs
CC BY-SA 4.0
2018-08-21T10:14:59.577Z
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.
Dan
CC BY-SA 4.0
2018-08-21T10:39:52.027Z
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?
llrs
<phylogenetics><algorithms>
Stand alone chaining tool for existing blast hits?
# Stand alone chaining tool for existing blast hits?

(Asked by: username_0 on 2018-08-17)

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](https://gist.githubusercontent.com/dbolser/c0e9d570b7023997ca6488bc483d208c/raw/1afc051d356409d8521ff35be086ce6cc8ed27f2/dummy%2520data.txt). Background is [here](http://www.mi.fu-berlin.de/wiki/pub/ABI/GenomeComparisonP4/chaining.pdf)

**Tags:** phylogenetics, algorithms
> **Comments:**
> **username_1**: 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.  
> **username_0**: Ideally I'd like something I can understand in a short subroutine.  
> **username_1**: What is short? I find the question unclear to search for solutions or to build such short "subroutine".  
> **username_0**: 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.  
> **username_1**: 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?  

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## 0 answers

