Hello,
first of all thank you for looking into my question.
I am trying to compute the frequency of all amino acids in a given genera and compareM is giving me trouble so I would like to know if there is an alternative to this.
in addition, I am also trying to algin two genomes and detect the number of conserved protiens between the two genomes to calculate the percentage of conserved proteins (POCP) which is a way to tell if two genomes belong to the same genera. this feature is present in compareM but I cannot seem to get it to work properly and until now I cannot figure out why or how to fix it.
in case you were wondering, appears to be installed properly but when I try the aai wf I don't get a summary tsv file. it appears that the script shutsdown mid processing and is marked as complete.
to summarize, if one can suggest tools for computing amino acid content and possibly another tool where it is possible to align two genomes and determine the genes based on alignment coverage and similarity.
thank you for your time.
It seems to be a problem with diamond. Try blastp instead
thank you for replying.
I was actually using blastp,
here is my script.
comparem aai_wf . aai_output_pocp --file_ext fasta --cpus 32 --evalue 0.00001 -p 40 -a 50 -x fasta --proteins --blastp -c 10 I have been using blastp all along.