Problem while using BPGA-Version-1.3 for pan bacterial genome analysis

Question

[ymir.dx]

I am trying to find similar and non-similar genes by analyzing whole genomes of 147 strains. I am using BPGA-Version-1.3. The problem which I am facing is that in some of the genebank files it gives the error "There were errors in the file:(filename). I even tried up upload the fasta file of the same strain to RAST server and download.gb file after annotation. But BPGA gives same error with that file also.

Here is the link to the image showing the error which I am facing

https://i.imgur.com/g84aYkw.jpg

Is there any way to fix this error or to fix my genebank files with a software or manually.

Please Help.

[rohitsatyam102]

I am facing same problem. Did you find the solution?

Answer 1

[mayankg.it.bhu]

You can ask that to the author of the paper, although they have mentioned that NCBI GenBank File (.gbk/.gbff) format required or you can use other formats which are mentioned on this web link: https://sourceforge.net/p/bpgatool/wiki/Home/

Regard Mayank

[rohitsatyam102]

I figured it out. The BPGA works well only with GenBank fileformat only for some reason and throws error for FASTA files. The error was the presence of a blank line at the end of Gbk file.

Thanks Mayank BTW

[deblinaroy164.1995]

Did you still find out the same problem during uploading of faa files?

Answer 2

[deblinaroy164.1995]

please tell me the steps of downloading .gbk files