Pseudoknot Finder tool

[Eli_Fisker]

@DigitalEmbrace, from top of my mind the human RefSeqGenes I have been handling so far have had a range from around 10000 to 240000 bp. +/-

There will likely be ones that have extremely long introns. I think I recall one gene that took real long time to make. Looked it up and it is Titin. It actually isn’t too bad:

In such cases, I would just up the filter level. As of now we can’t do complete scans. The pseudoknots we find are going to be used for finetuning pseudoknot finding algorithms. So as long as I get a proper amount of pseudoknots for a gene, I’m happy, even thought I know it is not a complete scan. For a short gene, I want pseudoknots enough = low filter level. For really large genes, I just want the largest pseudoknots, as they will likely also be the best targets.

I totally agree with submitting a specific gene variant of a disease that has ones interest. Thumbs up on that.

Thx for the UCSC website link. Looks complex, but potentially also very interesting. Especially gene network and the linking to outside resources.

For F8 I found an paper from 2010 saying that:

“At present, more than 1209 mutations within the F8 coding and [untranslated regions have been identified and listed in the F8 HAMSTeRS mutation database: a comprehensive international database, HAMSTeRS (The Hemophilia A Mutation, Structure, Test and Resource Site), which lists hundreds of mutations yielding the hemophilia phenotype established and maintained in the United Kingdom.”
Molecular genetics of hemophilia A: Clinical perspectives

So many different mutations of the same gene, can end up giving the same disease.

Ah, I see you meant to find the coding sequence with X01179 only. The way I would get to the mRNA via NCBI is to do this:

And then I would pick variant 1. They are all refseq’s.

[Eli_Fisker]

The nice shortcut I had to finding refseqgenes in NCBI doesn’t seem to be working more. I have found a work around for now. Search like this. Gene name + refseqgene in the search field:

Often this will land you directly on the specific refseqgene site:

Thx to @mjt and @whbob who have been helping with the rare disease genes.

mjt found a case where a refseqgene didn’t pop up immediately after doing this. In this case there is a different workaround to get to it. Choose Genomic:

I pick genomic, because I don’t want the protein - that is all amino acids. Also I don’t want the transcript - this is just the mRNA, which is way shorter and without the introns. I want the entire gene. With all its potential pseudoknots.

I have found another method that seems to yield success more often. Choose Advanced search:

Throw in the gene name in the first search field and refseqgene in the second field. Click Search.

And voila:

Later note: Everything seems to be normal now. It is possible find refseqgenes as I first demonstrated, by just pasting in the gene name.

[jandersonlee]

The latest ArcKnot version now has a Pseudo-knot finder mode with the FASTA function.

You can paste FASTA formatted text into the Notes area and click on “FASTA” to split it into segments to be tested. By default it will use the >name header line from the FASTA block to create the title and description. You can also add a “title: my title prefix” and “desc: my desc suffix” in the Config area to add extra text to the the title and description areas as it processes them.

Hitting “Random” will process the segments to screen for pseudoknots. Click on “Prune” when it is done to eliminate non-knots and weak knots. If you want to change the knot strength threshold and don’t care about lab tail conflicts, you can add a “like: knot>3” or similar to the Config area before doing the “Random” check.

If you have a large FASTA block and want a random sample instead of all possible knots, use a Config setting like “sample: 20” to randomly pick 1/20 (5%) of the samples.

[jenni111]

https://eternagame.org/scripts/11720285

Is is possible to have an update to this script to reflect the 130 pk lab. As this script states it is for 100 bases. Sorry, I don’t know anything about coding.
Jenni

[jnicol]

It works automatically on any lab that has the purple do not care area to be used for designs. I should update the text description, but it will work as is. Note that only the first puzzle in round 3 has a usable design area that the pseudoknot finder script can use. Puzzles 2, 3 and 4 do not have the purple don’t care area, so the finder tool will not work with those puzzles.

[jenni111]

ok, thank you.