August 10, 2017 ademcan No comments

How to get a specific sequence (chromosome, start, end) from the command line?

In several of my projects, I have to focus on specific regions of a genome, let’s say while looking for binding peaks. It is quite common to download a full genome as a fasta file, or each chromosome separately from Ensembl or NCBI. However, it is difficult to get a specific region of a genome (chromosome, start, end). I didn’t find any easy solution for it so far. Therefore, I focused on using tools available directly from NCBI, the e-utilities.

To get a specific region of the genome one needs to know the GI identifier of the chromosome of interest. Let’s say we are interested in sequences from chromosome 2L of Drosophila melanogaster. The first step is to search for it on the Nucleotide database of NCBI.

Here, we have to note the GI identifier (667674288)

Then, the command to run is

efetch -db=nuccore -format=fasta -id=667674288 -seq_start=12200 -seq_stop=13000

This will return the sequence of chromosome 2L between positions 12200 and 13000 in fasta format as follow:

>AE014134.6:12000-12200 Drosophila melanogaster chromosome 2L

This command gets really handy when working with multiple regions. One could save all the regions of interest in a tab separated file with one column containing the start position and the other the end positions such as:

12000    12200
13500    13700

and then use awk to get the sequences for all those regions and save it as a fasta file:

awk '{ system("efetch -db=nuccore -format=fasta -id=667674288 -seq_start="$1" -seq_stop="$2" ") }' dmel_chr2L_peaks.txt > dmel_chr2L_peaks.fasta

Enjoy and let me know if you have any alternative solution for this problem.

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