{"name":"ApE","description":"A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly.","homepage":"https://jorgensen.biology.utah.edu/wayned/ape/","biotoolsID":"ape_plasmid","biotoolsCURIE":"biotools:ape_plasmid","version":[],"otherID":[],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_0578","term":"Plasmid map drawing"},{"uri":"http://edamontology.org/operation_0308","term":"PCR primer design"},{"uri":"http://edamontology.org/operation_0564","term":"Sequence visualisation"},{"uri":"http://edamontology.org/operation_0310","term":"Sequence assembly"},{"uri":"http://edamontology.org/operation_0365","term":"Restriction digest"}],"input":[],"output":[],"note":null,"cmd":null}],"toolType":["Desktop application"],"topic":[{"uri":"http://edamontology.org/topic_0196","term":"Sequence assembly"},{"uri":"http://edamontology.org/topic_2885","term":"DNA polymorphism"},{"uri":"http://edamontology.org/topic_0632","term":"Probes and primers"},{"uri":"http://edamontology.org/topic_3125","term":"DNA binding sites"},{"uri":"http://edamontology.org/topic_3168","term":"Sequencing"}],"operatingSystem":["Mac","Windows","Linux"],"language":[],"license":"Other","collectionID":[],"maturity":null,"cost":"Free of charge","accessibility":null,"elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[{"url":"https://github.com/mwdavis2/ApE","type":["Repository"],"note":null}],"download":[],"documentation":[],"publication":[{"doi":"10.3389/fbinf.2022.818619","pmid":"36304290","pmcid":"PMC9580900","type":[],"version":null,"note":null,"metadata":{"title":"ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program","abstract":"A plasmid Editor (ApE) is a free, multi-platform application for visualizing, designing, and presenting biologically relevant DNA sequences. ApE provides a flexible framework for annotating a sequence manually or using a user-defined library of features. ApE can be used in designing plasmids and other constructs via in silico simulation of cloning methods such as PCR, Gibson assembly, restriction-ligation assembly and Golden Gate assembly. In addition, ApE provides a platform for creating visually appealing linear and circular plasmid maps. It is available for Mac, PC, and Linux-based platforms and can be downloaded at https://jorgensen.biology.utah.edu/wayned/ape/.","date":"2022-01-01T00:00:00Z","citationCount":102,"authors":[{"name":"Davis M.W."},{"name":"Jorgensen E.M."}],"journal":"Frontiers in Bioinformatics"}}],"credit":[{"name":"Erik M. Jorgensen","email":"jorgensen@biology.utah.edu","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":[],"note":null}],"owner":"Chan019","additionDate":"2022-12-20T09:03:13.253951Z","lastUpdate":"2024-11-24T15:17:17.922714Z","editPermission":{"type":"public","authors":[]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":"tool"}