Entering edit mode
7.1 years ago
konstantinkul
▴
110
Hello, Did anybody has the error while the GenePrimp (http://www.nature.com/nmeth/journal/v7/n6/full/nmeth.1457.html) parsing the Blastp output at the first stage of analysis. I have the same issue by analysis both the gbk file from ncbi and the gbk file produced by Prokka. I also tested the different versions of Perl 5.8.5, 5.16, 5.24. I can't understand what is the problem. As I remember, a year ago everything was OK. I also found that analysis of fragmented prokaryotic genome with annotation was successful, but using complete genome (~1 Mb) fails.
Thank you in advance, for any suggestions.
I've just surfed my previous posts in BioStar and decided to explain how I solved this issue a year ago.
The problem was due to incorrect formatting of last releases of protein (nr) blast databases. When I extracted all sequence from NCBI blast database and again created the blast database but with old version makeblastdb. After this reformatting GenePrimp works fine.