Hi.
I have fasta file and I want to run the file in Blast2Go through galaxy for functional characterization. Plz guide me about the steps required for this purpose.
thx
Hi @humaira,
firstly you should run the NCBI BLAST+ blastx tool in order to map your FASTA sequences against a protein database (ideally SWISSPROT, but you can select more than one database in the Protein BLAST database option). In addition, you should select BLAST XML as the output format for this tool. Then you can use the Blast2GO on the results generated in the previous step.
Regards
1 Like
Hi @gallardoalba,
I tried bast2go as per your guidelines but this error appeared after using the NCBI blast +blastx output file with XML extension. Please guide how to fix it.
I am also sharing the file link here
https://usegalaxy.eu/datasets/11ac94870d0bb33ac3f6b626677349b3/display?to_ext=blastxml
Hi @Rezwan_Tariq,
it seems that there is a problem with that tool; I created an issue in order to report it: Problem with Blast2Go. I’ll inform you as soon as it is corrected.
Regards
1 Like
Hi@gallardoalba, I think this Blast2GO version needs to be updated because the current version is outdated.
1 Like
So in this case is there is no need for makeblastdb prior to blastx?
Before employing Blastx within the Galaxy platform, it is advisable to establish a local nr (non-redundant) database. To achieve this, it is necessary to modify the “blastdb_p.loc” file using the vim text editor, adding the local nr protein sequences obtained from the National Center for Biotechnology Information (NCBI).
Consolidating Blast2GO not working
Blast2Go is not available for now at the public Galaxy servers.
ps: In Galaxy, the larger databases are natively indexed. For custom databases, use makeblastdb tool for the indexing, then the BLAST+ tools. All is through the UI for end users.