Dear Ole,
Thank you for introducing “OrthAgogue” software for biologist like us. In
my project, I am trying to identify ortholog sequences in twelve fish species,
however I have no so much experience in finding ortholog protein sequence for
multiple species. To our knowledge on this subject, only four software were
developed for such a purpose (for multiple species); OrthoMCL,Multiparanoid,
Proteinortho and OrthoAgogue. Due to its efficiency and applicability in large
dataset, I decided to use OrthoAgogue. In our project, a protein fasta file of
a fish species (obtained from de novo transcriptome assembly) will be searched
against to 11 fish protein fast files (obtained from Ensemble non-redundant
protein fast files) to find ortholog protein sequences.
As you well know, we must do a blast analysis (first I create a blast database
using makeblastdb option and then, by using blastp option with suitable
parameters, program start to matches the sequences).
My question are;
1) Which should protein fast file be database ? Can I select randomly ? for
instance, my fast file.
2) In your manual, there is an command line like; “orthAgogue -i myblast.out
-e 6 -O myoutdir”. My question is regarding the “my blast.out”;
Do I obtained this “my blast.out” after blastp analyses of each fish
species (pairwise like search,for example, my fish (anchovy, database) vs
zebrafish) or obtained via comparing all fishes against the database (for
example, database (my fishes) vs zebra fish, puffer fish, etc…).
If you help me about this issue and provide a blastp command for multiple
species, I will greatly appreciate.
Best Regards,
Vahap ELDEM
Department of Biology, Istanbul University, TURKEY
Original issue reported on code.google.com by eldemva...@gmail.com on 13 Jul 2015 at 2:48
Original issue reported on code.google.com by
eldemva...@gmail.comon 13 Jul 2015 at 2:48