Summary.txt - conserved regions question

[KristinaGagalova]

Hi,
I am having some high scores for the conserved regions from KIPEs.

ID      Gene    Similarity      ConservedResidues       ConservedRegions
geneA      PAL_1   81.25897772527608       100.0   10000.0
geneB      PAL_2   79.7446236531842        100.0   10000.0
geneC      PAL_3   79.60565251499916       100.0   10000.0

Is that a percentage that needs to be normalized or it's a score value? Thank you in advance

[KristinaGagalova]

I also have a question about the Similarity score - what reference species are you using to estimate that? Is this the blast identity or positive scoring value?
Thank you in advance

[bpucker]

Hi Kristina,

The similarity is already a relative value ranging from 0 to 100%. It is calculated based on a global alignment containing all bait sequences and the candidate sequence. This value is the average similarity between a candidate sequence and and all bait sequences. Therefore, it does not depend on a single reference sequence.

The information about the conserved residues is also relative ranging from 0 to100%. This is the proportion of functionally relevant amino acid residues that were detected in your candidate. It should be 100% in most cases. Sometimes an enzyme might be functional with one of these residues missing if previous studies considered an amino acid crucial which is actually not essential for the enzyme function.

Finding 3 PALs looks fine. Many species have multiple PAL copies.

Best wishes,
Boas

[KristinaGagalova]

Hi Boas,
That looks good!
I was just wondering why the last column is 1000 (I believe it should be normalized to 100 as for percent).
Also, just to understand better - you are not adding the conserved residues to the last baits? ie. OMT, UGT etc.
Thanks
Kristina

[bpucker]

Hi Kristina,
Thanks for your comment. You discovered a bug. The value was multiplied with 100.0 twice. It is fixed in the new version v0.34. Now, you should get results between 0 and 100.
Best wishes,
Boas