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从NCBI批量下载序列

已有 4802 次阅读 2016-12-30 23:16 |个人分类:生物信息学与计算生物学|系统分类:科研笔记

好久没有玩过大量序列了,发现之前的脚本不管用了,所以从bing上又学习了一遍。下面是一位大神总结的几种最简单的方法。From https://edwards.sdsu.edu/research/ncbi-sequence-or-fasta-batch-download-using-entrez/
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.




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