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 Open-Source — ultimaker ultimaker (Ultimaker) / debian-backup — Project
A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.
Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).
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Debian logo prodigal  1:2.6.3-4

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One-liner (summary)

Microbial (bacterial and archaeal) gene finding program

Description

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:

Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.

Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).

Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.

GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.

Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.

Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.

License

Unknown

Size

917.5 KB

Downloads

0

Tags

debian/buster deb arm64 main latest

Status  Completed
Checksum (MD5) c341a04f8b773be9586320977f3dafc2
Checksum (SHA-1) 2a32251d0eda187d8a84823cd5920323afc0b06a
Checksum (SHA-256) eef4c49d2d4366e8b836eb806508957ae0582c693800351d8cf1ce309639dc8f
Checksum (SHA-512) 19803ba5b022a570bd4b206d97877ad72278be7ccb1c4c21b0b47e951acfe192d2…
GPG Signature
Download
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 6 months, 3 weeks ago
Uploaded By alex-borro
Slug Id prodigal_263-4_arm64deb-js84
Unique Id Vh1P24IdtfKs
Version (Raw) 1:2.6.3-4
Version (Parsed)
  • Epoch: 1
  • Major: 2
  • Minor: 6
  • Patch: 3
  • Pre (Str): (empty)
  • Pre (Num Array): 4
  • Type: SemVer (Compat)
  extended metadata
Homepage http://prodigal.ornl.gov/
Installed Size 11.0 MB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg prodigal_2.6.3-4_arm64.deb 0
917.5 KB 		md5 sha1 sha256 sha512
Package Contents (prodigal_2.6.3-4_arm64.deb)
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This package has 18 files/directories.

Dependencies

1

Checksum (md5)

1be18b11824a57b33e2b5511f29c16a4

Depends
libc6 >=2.17
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[![This version of 'prodigal' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)
|This version of 'prodigal' @ Cloudsmith|
.. |This version of 'prodigal' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'prodigal' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/1:2.6.3-4/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'prodigal' @ Cloudsmith" /></a>

rendered as: This version of 'prodigal' @ Cloudsmith

To embed the badge for the latest package version, use the following: 

[![Latest version of 'prodigal' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)
|Latest version of 'prodigal' @ Cloudsmith|
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   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/
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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prodigal/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prodigal/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'prodigal' @ Cloudsmith" /></a>

rendered as: Latest version of 'prodigal' @ Cloudsmith

These instructions assume you have setup the repository first (or read it).

To install/use prodigal @ version 1:2.6.3-4 ...

To install packages, you can quickly setup the repository automatically (recommended): 

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical): 

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages: 

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update
sudo apt-get install prodigal=1:2.6.3-4
Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.
Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).
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