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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).

Debian logo sim4  0.0.20121010-5

One-liner (summary)

tool for aligning cDNA and genomic DNA

Description

sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).

sim4 employs a blast-based technique to first determine the basic matching blocks representing the "exon cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments.

License

Unknown

Size

379.7 KB

Downloads

2

Status  Completed
Checksum (MD5) 8a2b5fc6c990cbcaa0855725f3450222
Checksum (SHA-1) 66e82106aa0e7e2e1f941fa50c587a91912b46ef
Checksum (SHA-256) cd9b043e5cf06e788c3489546a78e41d525ba1619af5503fd0a489a605c182f2
Checksum (SHA-512) 69feb9b9e7bbe1ffdb70ec356515afcc5b955e92fde44cadef93fe69412caa9c37…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 11 months ago
Uploaded By alex-borro
Slug Id sim4_0020121010-5_armhfdeb-2rcg
Unique Id TikkXjYXhSOV
Version (Raw) 0.0.20121010-5
Version (Parsed)
  • Major: 0
  • Minor: 0
  • Patch: 20121010
  • Pre (Str): (empty)
  • Pre (Num Array): 5
  • Type: SemVer (Strict)
  extended metadata
Homepage http://globin.bx.psu.edu/html/docs/sim4.html
Installed Size 416.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg sim4_0.0.20121010-5_armhf.deb 2
379.7 KB
md5 sha1 sha256 sha512
Package Contents (sim4_0.0.20121010-5_armhf.deb)
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This package has 16 files/directories.

Dependencies

1

Checksum (md5)

489b1fab53f4217d0d564d99bf67bb7f

Depends
libc6 >=2.7

You can embed a badge in another website that shows this or the latest version of this package.

To embed the badge for this specific package version, use the following:

[![This version of 'sim4' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)
|This version of 'sim4' @ Cloudsmith|
.. |This version of 'sim4' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'sim4' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/0.0.20121010-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'sim4' @ Cloudsmith" /></a>

rendered as: This version of 'sim4' @ Cloudsmith

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

[![Latest version of 'sim4' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)
|Latest version of 'sim4' @ Cloudsmith|
.. |Latest version of 'sim4' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'sim4' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/sim4/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'sim4' @ Cloudsmith" /></a>

rendered as: Latest version of 'sim4' @ Cloudsmith

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

To install/use sim4 @ version 0.0.20121010-5 ...

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 sim4=0.0.20121010-5
Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.
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