You must think that  I am pedantic and stubborn ... well, that's me ...

I put the pieces together as you painstankingly taught me to do.

You have already stressed that the following Fasta files contains EXPERIMENTALLY VALIDATED miRNAs.
"ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/mature.fa.gz"
"ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/maturestar.fa.gz"

However, if I got it right, the Homo Sapiens PREDICTED miRNAs and genes dataset from Ensembl  that looks like the following, contains
associations (miRNA,gene) that for sure have been PREDICTED but not necessarily EXPERIMENTALLY  VALIDATED. Am I right ?

        GROUP             SEQ  METHOD      FEATURE CHR     START       END STRAND PHASE   SCORE   PVALUE_OG   TRANSCRIPT_ID EXTERNAL_NAM
1  Similarity     mmu-miR-707 miRanda miRNA_target   2 120824620 120824640      +     . 15.3548 2.79654e-02 ENST00000295228      INHBB
2  Similarity     hsa-miR-647 miRanda miRNA_target   2 120824263 120824281      +     . 16.3205 3.70140e-06 ENST00000295228        INHBB

Therefore my data blocks associate  miRNAs with a number of genes 3'UTR regardless of their VALIDATION. Presumably just a subset of all predicted 
are actually VALIDATED. 
This is no time or energy wasted because this bulk miRNA --> genes 3'UTR  data will be very useful for testing the program that is being developed.
However, getting just the VALIDATED miRNA --> genes 3'UTR is step-1 to train the algorithm.
A Bioinformatic guy, who is very good with Genetic and Evolutionary algorithms, is developing a program aimed at predicting miRNA targets.
>From my understanding, these algorithms are similar to Neural Networks, thus they have to be trained first, then tested on a supervised set.
If these two stages are performed correctly, the algorithm should then discriminate on the basis of  rules learnt  from the training.

Bottomline, I guess I can't spare myself from dealing with miRecords XLS file as well .... 
Basically I should use the miRecords VALIDATED data to screen the information I am getting through the procedure your taught me.
The downside of this further mapping is that miRecords apparently does not offer an ftp or any other automatic data transfer protocol.

Kind regards,
Maura




tutti i telefonini TIM!


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