Choosing tool for DNA secondary structure stem-loop prediction

Question

[Anand Rao]

I am looking to identify a stem-loop DNA secondary structure in genomic DNA (not RNA) sequences.

This structure is usually ~ 10nt from the 3' terminus, and it is usually ~15-20nt long.

There seem to be > a dozen options to predict secondary structure in DNA (like at this page: https://omictools.com/dna-structures-category)

https://omictools.com/unafold-tool

https://omictools.com/do-x3dna-tool

https://omictools.com/3dna-tool

https://omictools.com/curves-tool

https://omictools.com/3d-dart-tool

https://omictools.com/cgdna-tool

https://omictools.com/mint-4-tool

https://omictools.com/dnashaper-tool

https://omictools.com/sist-tool

https://omictools.com/cgheliparm-tool

https://omictools.com/yup-tool

https://omictools.com/multirnafold-tool

So I'm seeking advice forum members' advice for what would satisfy the following criteria:

1. command line use,

2. fast & high throughput to process entire genomes,

3. prefer multi-threaded option to speed up runs,

4. will return palindrome and sequence of stem-loop,

5. prefer it will allow palindrome length as pre-filter for the run, (though post-processing of results is OK, but not preferred),

6. prefer it will allow palindrome position with respect to DNA sequence 3' end, (though post-processing of results is OK, but not preferred), and

7. returns score of predicted secondary structure, in case I need / want to use that info later.

8. And anything else I might missed out, which you think would be important for my goals.

I've never predicted DNA secondary structure, much less used software like UNAfold or Mfold, or EMBOSS's 'einverted' or 'palindrome'. So, I look forward to your responses. Thanks!

Answer 1

[Anand Rao]

Answering my own question: DNA Punctuation looks promising

More info at : http://www.dnapunctuation.org/ and https://github.com/mariapoptsova/dnapunctuation

Example of it's application found in this paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135761/#Sec17 # free access, but additional info to access this paper is as follows:

BMC Genomics. 2016; 17: 992. Published online 2016 Dec 3. doi: 10.1186/s12864-016-3344-4. PMCID: PMC5135761. PMID: 27914481