cobot-tools: Biological data file formats and IO

[ bio, bsd3, library ] [ Propose Tags ]

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Dependencies array (==0.5.*), base (>=4.7 && <5), bytestring, cobot, containers (>= && <0.7), data-default, data-msgpack (>=0.0.9 && <0.1), deepseq (==1.4.*), lens (>=4.16 && <5.0), mtl (>=2.2.1 && <2.3.0), regex-tdfa, text [details]
License BSD-3-Clause
Copyright 2018-2019, Less Wrong Bio
Author Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov
Category Bio
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Source repo head: git clone
Uploaded by ozzzzz at 2019-12-31T08:50:23Z
Distributions NixOS:
Downloads 1335 total (12 in the last 30 days)
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  • Bio
    • Tools
      • Sequence
        • CodonOptimization
          • Bio.Tools.Sequence.CodonOptimization.Algo
          • Bio.Tools.Sequence.CodonOptimization.Constants
          • Bio.Tools.Sequence.CodonOptimization.Types
        • Primers
          • Bio.Tools.Sequence.Primers.Constants
          • Bio.Tools.Sequence.Primers.Optimization
          • Bio.Tools.Sequence.Primers.Properties
          • Bio.Tools.Sequence.Primers.Types
        • ViennaRNA
          • Bio.Tools.Sequence.ViennaRNA.Cofold
          • Bio.Tools.Sequence.ViennaRNA.Fold
          • Internal
            • Bio.Tools.Sequence.ViennaRNA.Internal.Cofold
            • Bio.Tools.Sequence.ViennaRNA.Internal.Fold
            • Bio.Tools.Sequence.ViennaRNA.Internal.RNALike


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Tools for computational biology

Software required to use cobot-tools


ViennaRNA is a library that already contains lots of useful algorithms that work with RNA sequences. We use it in order to make tools from cobot-tools better.

Installation guide for Linux can be found here.

Some issues occur when you try to install ViennaRNA for MacOS. If you want to avoid them, use the following guide.

Installation of ViennaRNA for MacOS

Installation of ViennaRNA for MacOS can be done in following steps:

  1. Download library. Here is the link for version 2.4.13.
  2. Unpack it.
  3. Go to the directory, where archive has been unpacked.
  4. Run command ./configure --without-perl --without-python.
  5. Remove field libRNA_la_LDFLAGS and flag -static from the file src/ViennaRNA/
  6. Due to us having changed .am-file, it is needed to install following packages: autoconf and automake. In order to do it, run command: brew install autoconf automake.
  7. Run in the root of library command autoreconf.
  8. Compile library using command make -j8 (j8 - flag that allows us to compile code using 8 jobs).
  9. Run command make install.

Tools of cobot-tools


Given 'DNA' sequence and position in that sequence designs forward primer for that sequence. Primer will start at the given position.