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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 ncbi-epcr  2.3.12-1-7

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One-liner (summary)

Tool to test a DNA sequence for the presence of sequence tagged sites

Description

Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.

The new version of e-PCR implements a fuzzy matching strategy. To reduce likelihood that a true STS will be missed due to mismatches, multiple discontiguous words may be used instead of a single exact word. Each of this word has groups of significant positions separated by 'wildcard' positions that are not required to match. In addition, it is also possible to allow gaps in the primer alignments.

The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database.

This program is retired upstream and it is suggested to use Primer-Blast https://www.ncbi.nlm.nih.gov/tools/primer-blast/ instead.

License

Unknown

Size

107.1 KB

Downloads

1

Tags

debian/buster deb arm64 main latest

Status  Completed
Checksum (MD5) c8d872883a66a0b3d1e37684054c8e96
Checksum (SHA-1) acd01c65eeaba7f5d4d468ad0c9189a1ef57657e
Checksum (SHA-256) c5a147e457da1ea9840a61cfc9c52cdf07ed1db6aa3ed8379c0d6bdfcc2090ed
Checksum (SHA-512) 4534d8fd9598708e5aa57cf4e97a7e21ab5fe3f68d9cac29769736f110b3091ffc…
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 10 months ago
Uploaded By alex-borro
Slug Id ncbi-epcr_2312-1-7_arm64deb-bfzx
Unique Id FDsVHclBLxbg
Version (Raw) 2.3.12-1-7
Version (Parsed)
  • Major: 2
  • Minor: 3
  • Patch: 12
  • Pre (Str): (empty)
  • Pre (Num Array): 1.7
  • Type: SemVer (Strict)
  extended metadata
Homepage https://www.ncbi.nlm.nih.gov/tools/epcr/
Installed Size 421.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
Source epcr
pkg ncbi-epcr_2.3.12-1-7_arm64.deb 1
107.1 KB 		md5 sha1 sha256 sha512
Package Contents (ncbi-epcr_2.3.12-1-7_arm64.deb)
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This package has 22 files/directories.

Dependencies

4

Checksum (md5)

946738e128cac6456533faddcfb7412c

Depends
libc6 >=2.17
Depends
libgcc1 >=1:4.2
Depends
libstdc++6 >=5.2
Suggests
bioperl
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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/ncbi-epcr/2.3.12-1-7/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/ncbi-epcr/2.3.12-1-7/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'ncbi-epcr' @ Cloudsmith" /></a>

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|Latest version of 'ncbi-epcr' @ Cloudsmith|
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rendered as: Latest version of 'ncbi-epcr' @ Cloudsmith

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

To install/use ncbi-epcr @ version 2.3.12-1-7 ...

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 ncbi-epcr=2.3.12-1-7
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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