How to make .pal extension File from .seq.gz files

Question

[dpktiwari168]

Hello, I was trying to make a database for the bacterial sequences. So for that, I have downloaded the Bacterial sequences files from Genbankftp.ncbi.nlm.nih.gov). that are in .seq.gz file format. My question is that How can I convert these sequences files into a single .pal file. I was trying to do this task by MultigeneBlast software as it has an option by which it can do that automatically but it constantly gets failed during the final .pal file generation Part. Please let me know if anyone having an idea about that or anyone who has used Multigeneblast software.

Thanks and Regards Deep

[Joe]

You probably just need to decompress the files from .gz format before building the database. Pal files will probably be spit out during the database build step.

[dpktiwari168]

Thanks for your response. But its not working means after unzipping the .seq.gz files I have got .seq files which was again of no use because the tool which I want to use only considers .pal extension file. ya one way is that if I could have .gbk extension files of all those .seq files I can try to use those files for creating .pal file because the tool have an option to do that. If you know any tool or software or any code which can do do the same then Please let me know. It would be very helpful.

Thanks and Regards Deep

[Joe]

You need to make a blast database. I think, MultiGeneBlast simply uses normal blast databases, but the provided scripts typically take GBK files.

You should be able to generate a .pal by running makeblastdb on your seq files.