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Old 12-12-2013, 11:43 PM   #1
garethboy
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Default How to extract out a section of nucleotide sequence from the entire genome

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. :-)
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Old 12-12-2013, 11:57 PM   #2
rhinoceros
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You could do it with for example esl-sfetch. Or, if there are no linebreaks in your fastafile, you could simply:

Code:
grep -v '>' yourFastaFile.fasta | cut -c 501-12399 > theSubSequenceWithoutHeader.fasta
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Old 12-13-2013, 12:19 AM   #3
dpryan
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Alternatively just use samtools faidx:

Code:
samtools faidx sequence.fasta contig_name:n1-n2 > extracted_sequence.txt
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Old 12-13-2013, 12:28 AM   #4
garethboy
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thanks to both of you guys. Got my problem solved. =)
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