SynChro input files
1
1
Entering edit mode
2.6 years ago
jmah ▴ 20

I'm trying to use SynChro, a program to analyze synteny. It uses CHROnicle to make 3 input files which it creates from Genbank .dat files or EMBL .embl files. I cannot find either of these files as provided by Genbank or EMBL. However, Genbank provides a .gbff file that seems to be the current "Genbank" flat file format, while EMBL provides a .dat (confusingly) that looks to be similar in format to the .embl. Unfortunately, neither of these work with CHROnicle.

Has anyone managed to get SynChro to work? How did you find/convert the right file types?

Many thanks!

SynChro file conversion • 708 views
0
Entering edit mode
4 months ago
Jerobou • 0

Dear jmah,

I also struggled to make synchro work, precisely because I couldn't find a correct format that can be taken as an input for Synchro. The ConvertGbk.py and ConvertEMBL.py indeed seem to take as input very peculiar genbank and embl input files, that could be defined as "annotated". To make it work, I took the genomes (also work with unique assemblies parts) from the ensembl database. As an example, I downloaded the genbank files from H. sapiens (link: http://ftp.ensembl.org/pub/current_genbank/homo_sapiens/) and used the ConvertGbk.py code to translate them in a "Synchro-wise" format. And it worked !

I know this thread is a little old, but I hope this solution will help you or any other person struggling with the wonderful Synchro software.

Regards,

Jerobou

0
Entering edit mode

Thank you! It is a little old but I really appreciate your help! Better late than never!