Package: wnpp Severity: wishlist Owner: Daniela Moreira Mombach <danielamomb...@gmail.com> X-Debbugs-Cc: debian-devel@lists.debian.org, danielamomb...@gmail.com
* Package name : sideretro Version : 1.1.4 Upstream Contact: Thiago L. A. Miller <tmil...@mochsl.org.br> * URL : https://github.com/galantelab/sideRETRO * License : GPL-3+ Programming Lang: C Description : pipeline for detecting Somatic Insertion of DEnovo RETROcopies sideRETRO is a bioinformatics tool designed for the detection of somatic retrocopy insertions, also known as retroCNVs, in whole genome sequencing (WGS) and whole exome sequencing (WES) data. . Retrocopies, also known as processed pseudogenes, are sequences derived from protein-coding genes, generated by the duplication of these genes through the transposition of their mature messenger RNA via the LINE-1 enzymatic machinery. Retrocopies can be fixed, meaning they are present in all genomes of a given species (including the species' reference genome), or unfixed (polymorphic, germline, or somatic), in which case they are referred to as retroCNVs. While fixed retrocopies have received considerable attention in the scientific community, knowledge of retroCNVs remains limited, largely due to the lack of specialized bioinformatics tools for their identification and annotation in DNA sequencing data. . sideRETRO is a dedicated computational algorithm that detects retrocopies absent from the reference genome but present in WGS and WES data from other individuals. In addition to identifying retroCNVs, sideRETRO annotates several characteristics associated with these events. It provides information on the genomic coordinates of the insertion, including chromosome, insertion point, and DNA strand. It also determines the genomic context of the event (exonic, intronic, or intergenic), performs genotyping (presence or absence), and provides haplotyping information (homozygous or heterozygous).
