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Xiangyang1984 / Gcluster

A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
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Questions regarding interested_gene_file #3

Open ZepingQu opened 4 years ago

ZepingQu commented 4 years ago

Hello Xiangyang,

Thanks for creating and sharing this tool. I have a few questions regarding using Gcluster, first is in terms of using interested_gene_file.pl, are we supposed to create a fasta file by our own containing the LOCUS tag and protein sequence? Do you have an included script in Gcluster for doing that? Secondly, as I'm thinking of comparing biosynthetic gene clusters, some of the gbk files in my database have identical LOCUS tags, would this situation cause any unwanted crashes from Gcluster?

Kindly regards

Gcluster的作者您好，

非常感谢您能够制作并分享Gcluster。关于Gcluster，我有几个问题希望能够请教您：第一是请问运行interested_gene_file.pl所需的fasta文件是需要包含所有想要比对的gbk文件中的LOCUS标签和蛋白质序列吗？您的package中有包含自动生成这一fasta文件的script吗？第二是请问如果我的database当中有几个gbk文件有相同的LOCUS标签会导致程序运行错误吗？谢谢！

Xiangyang1984 commented 4 years ago

Dear ZepingQu,

Thanks for your interest in Gcluster. interested_gene_file.pl needs two input files to work: 1. a directory containing gbk files you wanted to analyze, 2. a protein sequneces file used as database. As to the fasta file you mentioned here, I do not know what you means? As to the second question, we did not test whether it would get an error if serveral gbk files contains the same locus tag.

Sincerely， Xiangyang Li lixiangyang@fudan.edu.cn