Extraction of Inverted Repeat Sequences within a list of oligonucleotides
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3.9 years ago

Hi all,

I am trying to extract the sequences of hairpin forming regions from a list of oligonucleotide sequences between 23-100 bases in length. The sequences are in table format consisting of coordinates (sequence ID) and sequence columns.

In my output, I would like to get the sequence ID, hairpin-forming sequence, length of stem, and length of loop within the oligonucleotide.

So far, I have tried using the eInverted and palindrome tools from EMBOSS, which give me the inverted repeats but the output is not in the format I desire.

Any help is greatly appreciated.

Thanks, Sub

inverted repeats IR repeat emboss einverted • 966 views
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Please post example input data and expected output

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