How to extract out a section of nucleotide sequence from the entire genome

[garethboy]

Hi all,

In a single contig of ~6 Mbp, I would like to extract out the sequence from nucleotide #N1 to #N2 (e.g. nucleotide number 501 to 12,399). May I know how am I going to do this?

I am very new in the bioinformatics field. Hope you all can help me. :-)

[rhinoceros]

You could do it with for example esl-sfetch. Or, if there are no linebreaks in your fastafile, you could simply:

grep -v '>' yourFastaFile.fasta | cut -c 501-12399 > theSubSequenceWithoutHeader.fasta

[dpryan]

Alternatively just use samtools faidx:

samtools faidx sequence.fasta contig_name:n1-n2 > extracted_sequence.txt

[garethboy]

thanks to both of you guys. Got my problem solved. =)