从NCBI批量下载序列

最新推荐文章于 2024-09-02 13:29:44 发布

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最新推荐文章于 2024-09-02 13:29:44 发布

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本文介绍三种从NCBI数据库批量下载多个序列的方法：通过Batch Entrez网站、使用Perl脚本以及直接利用浏览器地址栏。这些方法适用于需要快速获取大量序列数据的研究人员。

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Three easy ways to download multiple sequences from NCBI

There are different ways of how to download multiple sequences from the NCBI databases in a single request.

1) Using the batch Entrez website

http://www.>ncbi.nlm.nih.gov/sites/batchentrez

2) Using Perl: (copy into your terminal and press return/enter)

perl -e 'use LWP::Simple;getstore("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&retmode=text&id=".join(",",qw(6701965 6701969 6702094 6702105 6702160)),"seqs.fasta");'

This takes the IDs separated by spaces and the filename of the fasta file with the sequences that will be generated (seqs.fasta). If you don’t try to get the nucleotide data, then you will have to change the database name as well.

3) Using your browser: (paste this to the address field)

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=fasta&retmode=text&id=6701965,6701969,6702094,6702105,6702160

This time the IDs are separated by commas. Same here, if you need to get data from a different database you just have to change that.

转载自：https://edwards.sdsu.edu/research/ncbi-sequence-or-fasta-batch-download-using-entrez/