A Python program to merge Sanger sequences: an update.

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS ACS Applied Bio Materials Pub Date : 2024-10-22 eCollection Date: 2024-01-01 DOI:10.7717/peerj.18363

Shiming Lin, Bifang Huang, Li-Li Zhao, Fei Xu, Danni Pan, Xuanyang Chen, Shiqiang Lin

{"title":"A Python program to merge Sanger sequences: an update.","authors":"Shiming Lin, Bifang Huang, Li-Li Zhao, Fei Xu, Danni Pan, Xuanyang Chen, Shiqiang Lin","doi":"10.7717/peerj.18363","DOIUrl":null,"url":null,"abstract":"Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":null,"pages":null},"PeriodicalIF":4.6000,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505972/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Applied Bio Materials","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.7717/peerj.18363","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATERIALS SCIENCE, BIOMATERIALS","Score":null,"Total":0}

引用次数: 0

Abstract

Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

用于合并 Sanger 序列的 Python 程序：更新。

基因克隆是研究基因结构和功能的重要步骤。为了验证基因序列，需要使用 Sanger 测序，这可能会产生几个重叠的测序文件，需要先合并这些文件才能与目标基因序列进行比对。此前，我们曾报道过合并 Sanger 序列的 Python 程序 (https://peerj.com/articles/11354/)，该程序可在命令行下运行，并在很大程度上依赖于 EMBOSS 套件。在这一更新版本中，我们对该程序进行了多项显著改进。它提供了一个用 tkinter 编写的图形用户界面（GUI），既方便又稳定。它不要求用户在执行合并之前重新命名输入序列。在执行方面，更新版利用 Python 函数（Align.PairwiseAligner）对相邻序列进行配对，更加灵活（可调整程序参数，即首次连续匹配碱基的数量）。新版程序大大方便了 Sanger 序列的合并，为基因研究提供了便利。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊