Data

Tools

Indexes

Applications

Experiments

Open Source Science

ribbon_1.2

Ribbons extracts all copies of mRNA ribosomal 16s from bacteria or archaea genomes

https://github.com/kjestradag/ribbon_1.2

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Ribbons extracts all copies of mRNA ribosomal 16s from bacteria or archaea genomes

Basic Info
  • Host: GitHub
  • Owner: kjestradag
  • License: gpl-3.0
  • Language: Perl
  • Default Branch: master
  • Size: 1.73 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created about 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

DOI

Ribbon (Ribosomal Bona-fide)

Karel Estrada && Enrique Merino
Instituto de Biotecnología, Universidad Nacional Autónoma de México

Introduction

Ribbons extracts all copies of mRNA ribosomal 16s from bacteria or archaea genomes, using conserved motifs in the 16S mRNA ribosomal to detect them in the genomes and evaluate the true regions that contain a copy of this.

The main purpose of Ribbons is to extract complete copies of the 16S, including its 3' prime, where the signature of the anti-Shine-Dalgarno sequence is found.

Requirements:

-Perl v5.8 or above

-Perl Modules: 

Getopt::Std

List::Util

The best way to install a perl module would be CPAN

-MEME Suite (tested on v5.0.1) software (http://meme-suite.org/doc/download.html)

Depending on which shell you have, please add these environmental variables:

In bash shell, could be .bashrc or .bash_profile add:

export MEMEribbon=/path/where/you/installed/ribbon_1.2/db

PATH=$PATH:/path/where/you/installed/ribbon_1.2/bin

Recommendations:

Please, make sure that everything is installed and running properly. Once you defined the environmental variables you can run the script "ribbon" to chech if everything it's okay. You can also run the example in the "example" folder, like this:

$ cd example

$ ribbon ecoli.fna ecoli

if everything worked well, the md5sum firm of generated file "ecoli.ribcompletetail.fna" must be equal to the md5sum firm in the "md5sumecoli.ribcomplete_tail.txt" file.

Citation

Estrada, K., & Merino, E. (2019). Ribbon (Ribosomal Bona-fide) (Version 1.2) [Computer software]. https://doi.org/10.5281/zenodo.7796827

Any questions:

Karel Estrada karel.estrada@ibt.unam.mx

Owner

  • Name: Karel Estrada
  • Login: kjestradag
  • Kind: user

Bioinformatician. Hardware enthusiast.

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Ribbon (Ribosomal Bona-fide)
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Karel
    family-names: Estrada
    email: karel.estrada@ibt.unam.mx
    affiliation: >-
      Instituto de Biotecnología, Universidad
      Nacional Autónoma de México
    orcid: 'https://orcid.org/0000-0002-7671-6959'
  - given-names: Enrique
    family-names: Merino
    email: enrique.merino@ibt.unam.mx
    affiliation: >-
      Instituto de Biotecnología, Universidad
      Nacional Autónoma de México
identifiers:
  - type: url
    value: 'https://github.com/kjestradag/ribbon_1.2'
version: '1.2'
doi: 10.5281/zenodo.7796827
date-released: '2019-01-08'

GitHub Events

Total
Last Year