Dear all who are have expertise in bioinformatic, i was beginner and i would like to ask, now i do genome analysis, i got results but unfortunately there were some miss annotation by blastp caused by incorrect previous database which two genes were predicted as single gene. So here i need your help to guide me how to do curating this miss annotation, it was impossible if i should do blastp one by one. Thank for your kind, best regards: SA
Hi,
You could do the functional annotation of already predicted genes via reciprocal best BLAST hits (RBHs). If you are familiar with the execution of scripts, I could send you a Python script to do this for two peptide sequence data sets based on BLASTp. This method is more tolerant regarding errors than a simple BLASTp search in one direction. However, it is almost certain that there will not be a RBH for each of your predicted genes.
Moreover, your annotation cannot be better than the annotation of your reference. It is only a way to transfer the previously produced annotation from another (model) organism to your project.
Dear Mr. Pucker, sure, it should be try, anyway i was poor in script
Hi,
Please find attached the script. It requires an installation of python 2.76+ and BLAST. The script identifies the RBHs between two multiple FASTA files containing peptide sequences. You can run the script like this:
python identify_RBHs.py --input1 --input2 --prefix
Let me know if you encounter any problems.
Best,
Boas
Other possibilty: transfer annotations from a single genome, a trusted one. In the process, filter source annotations by a criteria, for instance, 70% of identity and size simultaneosly. An opcional tool is pannotator. Just Google It.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics