{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/introgression-browser-high-throughput-whole","title":"Introgression Browser: High throughput whole-genome SNP visualization","arxiv_id":"1504.05612","date":"2015-04-21","proceeding":null,"authors":[],"abstract":"Breeding by introgressive hybridization is a pivotal strategy to broaden the\ngenetic basis of crops. Usually, the desired traits are monitored in\nconsecutive crossing generations by marker-assisted selection, but their\nanalyses fail in chromosome regions where crossover recombinants are rare or\nnot viable. Here, we present the Introgression Browser (IBROWSER), a novel\nbioinformatics tool aimed at visualizing introgressions at nucleotide or SNP\naccuracy. The software selects homozygous SNPs from Variant Call Format (VCF)\ninformation and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms\n(MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use\nof sliding windows, but if needed it can generate any desired fragmentation\npattern through General Feature Format (GFF) information. In an example of\ntomato (Solanum lycopersicum) accessions we visualize SNP patterns and\nelucidate both position and boundaries of the introgressions. We also show that\nour tool is capable of identifying alien DNA in a panel of the closely related\nS. pimpinellifolium by examining phylogenetic relationships of the introgressed\nsegments in tomato. In a third example, we demonstrate the power of the\nIBROWSER in a panel of 600 Arabidopsis accessions, detecting the boundaries of\na SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short\narm of chromosome 4. The architecture and functionality of IBROWSER makes the\nsoftware appropriate for a broad set of analyses including SNP mining, genome\nstructure analysis, and pedigree analysis. Its functionality, together with the\ncapability to process large data sets and efficient visualization of sequence\nvariation, makes IBROWSER a valuable breeding tool.","url_abs":"http://arxiv.org/abs/1504.05612v1","url_pdf":"http://arxiv.org/pdf/1504.05612v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"introgression-browser-high-throughput-whole","repo_url":"https://github.com/sauloal/introgressionbrowser","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"high","task_name":"Vocal Bursts Intensity Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}