I am new to working with the NCBI database so I am not sure how trivial this question is. I wanted to get DNA sequence of a specific version of the Xenopus tropicalis genome of a specific region (ie 1-100bp) without doing it manually each time (going on genome browser). I know there is a faster way and efficient way to do this through the command line but I found the NCBI tutorial hard to follow.
Samtools is a toolkit that includes a binary called
samtoools, which can be used to query a FASTA file — to extract a subsequence based on some coordinate range you specify.
If you do not have
samtools installed, you need to add it to your computer. For OS X, you could use Homebrew, for example:
$ brew install samtools
For Ubuntu, you could use
$ sudo apt-get install samtools
The next step is to download a reference assembly for your genome and genomic build-of-interest.
$ curl --output "XENTR_10.0_genome.fasta.gz" "http://ftp.xenbase.org/pub/Genomics/JGI/Xentr10.0/XENTR_10.0_genome.fasta.gz"
You could also dig through the NCBI site to get a similar link. It's the same idea — just change the web address, accordingly.
Indexing makes it possible to extract an arbitrary subsequence of interest from this FASTA file. You need to index, but you only need to do it once:
$ samtools faidx XENTR_10.0_genome.fasta.gz
This creates two new files:
Note: You need to keep these two files in the same directory as the original, compressed FASTA file
Now you are ready to query, or extract a subsequence of interest. If you wanted the first hundred bases of the first chromosome, for instance:
$ samtools faidx XENTR_10.0_genome.fasta.gz Chr1:1-100 >Chr1:1-100 cctcagcgtcttcttctttctgctcccactgcattagcatagggagagagggccacagag gctaggtagcattgccggctagcaatcttcagcgtcctct
The search term used here is
Chr1 with the chromosome of interest and
100 with the start and stop coordinates, respectively, of interest. Coordinates used with
samtools queries use a one-based indexing scheme.
Note: This uses the chromosome naming scheme in the
XENTR_10.0_genome.fasta.gz file (
Chr1, etc.). Other research groups (NCBI) might use different chromosome names. If you get your FASTA from somewhere else, investigate the FASTA file to determine the naming scheme being used.
If you want to redirect output to a file, use the output redirect operator (
$ samtools faidx XENTR_10.0_genome.fasta.gz Chr1:1-100 > mySubsequence.fa