add sequence and structure feature

[teresa-m]

We can give the RRI (sequence and structure) as feature, by using EDEN?

1. prepare the sequence:
   • use Intarna output hybridDP and subseqDP
   • repalce the & by x. and xN (x =5) r should be < x/2
2. run eden or vactorizer to genreate feature
3. find way to inccopate this featrues to the other feature

[martin-raden]

you forgot the

end extension! ;)

ACGU&GCGU  -->  NNNNNACGUNNNNNNNNNNGCGUNNNNN
((((&))))  -->  .....((((..........)))).....

i.e. xN + seq1 + 2xN + seq2 + xN

[martin-raden]

if possible

anchor features on non-N nodes only!

that way, we leave out all artificial eden features that start at an inserted N

[teresa-m]

you forgot the

end extension! ;)

ACGU&GCGU  -->  NNNNNACGUNNNNNNNNNNGCGUNNNNN
((((&))))  -->  .....((((..........)))).....

i.e. xN + seq1 + 2xN + seq2 + xN

Thanks :-)

[teresa-m]

if possible

anchor features on non-N nodes only!

that way, we leave out all artificial eden features that start at an inserted N

something to discuss with Stefan.

[teresa-m]

In script get_featurs.py additional features are added to the one IntaRNA generated.

[smautner]

https://github.com/teresa-m/RNA_RNA_binding_evaluation/pull/31

[teresa-m]

Graph-Kernal features are integrated