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There are many software applications such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:

  • Making maps of plasmids
  • Annotating plasmids with common features
  • Finding restriction sites
  • Mapping Sanger sequencing reads
  • Showing sequence, reverse complement of the sequence, translations in different frames
  • Designing primers for specific applications (such as Gibson cloning)

Is there a tool that does functions such as these, but runs from a command line?

Note: My intent is not so much to get recommendations for what to use, but to get an idea of what software is currently available. Obviously there exist many CLI tools which can be made to serve also these purposes, up to and including general purpose text editors like vi.

I'm interested in what effort has already been made to produce CLI software specifically intended for cloning (by which I mean the functions described above).

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    $\begingroup$ Why does it need to be command line? Are you trying to batch these operations? And it would seem like any command line implementation of these would have very complex commands. $\endgroup$
    – user137
    Nov 14 '14 at 21:33
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    $\begingroup$ I agree with @user137 on this! For protein alignment you have things like Clustal W/Clustal X, which you can find from clustal.org but for your request it's far too complicated and you might be better off with GUI such as the ones listed. Many, including myself use R for bioinformatics related work and I have came across this (bioconductor.org/packages/release/bioc/html/ecolitk.html), which can address one of your points but I don't know of any unified CLI for the points you have said. If this answers you question, please let me know so that I can post it as an answer. $\endgroup$
    – Behzad Rowshanravan
    Nov 14 '14 at 23:34
  • $\begingroup$ @user137 I suspect that I will find the command line to be a more efficient interface for these functions, and it would be much more convenient for integrating the tools into my own scripts. $\endgroup$
    – Superbest
    Nov 15 '14 at 23:33
  • $\begingroup$ @Bez I was aware of but not familiar with Bioconductor. If you could explain specifically what parts of the package perform the functions I want, that would be a great answer. Otherwise, I think just mentioning Bioconductor itself is a fair response. $\endgroup$
    – Superbest
    Nov 15 '14 at 23:36
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    $\begingroup$ I haven't worked with that specific package itself but if you have R or RStudio, which is my preferred IDE, you simply have to enter the command source("bioconductor.org/biocLite.R") command to upload the biocLite package and prepare R for download from the bioconductor database/depository and then execute the command biocLite("ecolitk"). Its mostly for plotting functions to work with circular genomics and can be used with other genomes/plasmids according to the package description bioconductor.org/packages/release/bioc/manuals/ecolitk/man/… $\endgroup$
    – Behzad Rowshanravan
    Nov 15 '14 at 23:53
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Making maps of plasmids Annotating plasmids with common features

Plasmapper works through commandline

Finding restriction sites

Simple regex searches can do that

Mapping Sanger sequencing reads

BLAST will do it.

Showing sequence, reverse complement of the sequence, translations in different frames

EMBOSS has a collection of tools for these things. (getorf is a tool for finding ORFs)

Designing primers for specific applications (such as Gibson cloning)

Primer3 works through commandline


You can just download the entire EMBOSS collection. It has many useful tools.

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  • $\begingroup$ +1 for plasmapper, but the others aren't quite what I'm looking for. They are general tools which, in principle (and with some work) can be adapted for the purposes I mention. They are not a streamlined pipeline explicitly designed for it. $\endgroup$
    – Superbest
    Nov 15 '14 at 23:46
  • $\begingroup$ I always used BLAST for aligning Sanger-sequencing reads. You should find a lot of tools in EMBOSS collection (usual stuff like finding ORF, Reverse complement etc). I don't think there is a tool for designing primers for Gibson assembly. BTW plasmapper also annotates common restriction sites. $\endgroup$
    – WYSIWYG
    Nov 16 '14 at 9:01
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For protein alignment you have things like Clustal W/Clustal X. Many, including myself use R for bioinformatics related work and I have came across this package which can be found in Bioconductor, which can address one of your points but I don't know of any unified CLI for the points you have said.

I haven't worked with that specific package itself but if you have R or RStudio, which is my preferred IDE, you simply have to enter the command 

source("bioconductor.org/biocLite.R")

command to upload the biocLite package and prepare R for download from the bioconductor database/depository and then execute the command 

biocLite("ecolitk")

It's mostly for plotting functions to work with circular genomics and can be used with other genomes/plasmids according to the package description.

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pydna is a python package designed for cloning. Disclaimer: I am the developer. It can be used in a Jupyter notebook to create executable scripts that result in the sequence of a some genetic construct. Restriction cloning, gibson assembly/homologous recombination are supported.

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    $\begingroup$ Welcome to Biology.SE. As written this would be more appropriate as a comment. We're looking for long answers that provide some explanation and context. Please don't post one-line or link-only answers; instead explain why your answer is right, ideally with citations. In this case I personally would preferred the question be closed as opinion based (off-topic), but since it wasn't you could provide a summary of what your package does and how it is an improvement over existing tools. ——— Please take the tour and consult the help center starting with How to Ask and How to Answer for details. $\endgroup$
    – tyersome
    Oct 23 at 19:04

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