pickbestpolish

PickBestPolish Installation On A Debian, Ubuntu, Kali And Raspbian

PickBestPolish Installation On A Debian, Ubuntu, Kali And Raspbian

pickBestPolish

batch spliced alignment of cDNA sequences to a target genome

Maintainer: Debian Med Packaging Team



Section: science

Install pickBestPolish

  • Debian apt-get install sim4db Click to copy
  • Ubuntu apt-get install sim4db Click to copy
  • Kali Linux apt-get install sim4db Click to copy
  • Raspbian apt-get install sim4db Click to copy

sim4db

batch spliced alignment of cDNA sequences to a target genome

Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences. While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features. This package is part of the Kmer suite.

Installation of latest pickBestPolish command is available for Debian, Ubuntu, Kali and Raspbian. You can copy the command for your OS from above and paste it into your terminal. Once you run the command it will download the 2022 latest package from the repository and install it in your computer/server.