Cut-off to choose the homology template using DIAMOND about carveme

[cdanielmachado]

Hi @hongzhonglu

You can see in this file how we invoke diamond:

https://github.com/cdanielmachado/carveme/blob/master/carveme/reconstruction/diamond.py

We are currently running diamond with these options: "--more-sensitive --top 10", which takes the top hits instead of using an arbitrary cut-off value.

You can try passing any arguments you want to diamond with the flag --diamond-args and see if other types of cutoff improve your annotations.

We tried with many different options, but this was what worked best for us. Since CarveMe uses the homology scores to assign reaction scores, the low homology genes generate small reaction scores, so they do not influence the final reconstruction so much.

[hongzhonglu]

@cdanielmachado Great thanks!

[hongzhonglu]

Hi @cdanielmachado
An another question. Do the homology scores mean the bitscores, which is obtained using diamond?
Thanks in advance!

[cdanielmachado]

Yes, the homology scores are the bitscores, sorry for not making that more clear on the paper.

[hongzhonglu]

Thanks very much!