https://github.com/imamachi-n/mirage

Comprehensive miRNA target prediction software
https://github.com/imamachi-n/mirage

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Comprehensive miRNA target prediction software

• Host: GitHub
• URL: https://github.com/imamachi-n/mirage
• Owner: Imamachi-n
• License: mit
• Created: 2015-08-21T10:15:20.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2015-09-11T09:50:43.000Z (about 9 years ago)
• Last Synced: 2023-05-22T07:32:06.525Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 215 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# MIRAGE #

**Comprehensive miRNA target prediction software**

###-prerequisite###

Python-3.x  

ViennaRNA  

PyYAML  

For Ubuntu,  

**ViennaRNA installation**

```

sudo apt-add-repository ppa:j-4/vienna-rna

sudo apt-get update

sudo apt-get install vienna-rna

```

**PyYAML installation**

```

sudo apt-get install libyaml-dev

wget http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz

tar zxvf PyYAML-3.11.tar.gz

cd PyYAML-3.11

sudo python3 setup.py install

```

**Download Conservation Score file**  

(1)Wigfix files (e.g.chr1.phyloP46way.wigFix.gz) are downloaded from the following HTML.  

```

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons46way/vertebrate/

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/vertebrate/

```

(2)The following scripts are run to prepare conservation score for RefSeq and miRBase transcriptome.  

```

python3 mirage_prepare.py phastcons_prep

python3 mirage_prepare.py phastcons_sizedown

python3 mirage_prepare.py phastcons_score_list

```

```

python3 mirage_prepare.py phylop_score_prep

python3 mirage_prepare.py phylop_sizedown

python3 mirage_prepare.py phylop_score_list

```