File format for plasmids in Vector NTI, Clone Manager etc - I'd like a compatible format with no/minimal data loss (Jul/21/2009 )

I've recently starting using software to plan molecular cloning strategies etc. I'm wondering about what file format to use. I prefer using Vector NTI, but others prefer Clone Manager. Thus, I'd like a file format that can be read by all major softwares. Is there a disadvantage to using, say, GenBank format instead of Vector NTI's native format? Will information be lost?

This is a major problem. AFAIK, most of the softwares have their own formats and can not be read by others except the sequence at the max. If you have any 'feature' on sequence then there is a good chance that it will be lost.

Since I started working with molecular biology, I am looking for some open source software decent enough to use, doesn't have any limitations for the platform you use. I am yet to find one.

As mentioned by noelmathur, the specialised formats of most of the softwares are mutually intelligible. Thus I would recommend using the GenBank or EMBL formats. You will not lose any features annotated on the sequence, however the colour and shape that these features are represented as will be lose.

All plasmid annotation software (or very close to that) will recognise the GenBank and EMBL format.

SnapGene Viewer was designed specifically to address this problem. It's free software (for both Mac and Windows) that allows you to create DNA map and sequence files, and to annotate them with features and primers. Then you can share the files with other scientists if they download the program at

http://www.snapgene.com/products/snapgene_viewer/

You can also export the maps in various formats, and you can export the sequences in GenBank format for import into other software.