Right, it’s been a couple months since I looked at ApE files but I think the LOCUS line had a couple of places where the spacing was off by one.

Even though it’s not technically correct, though, I think that’s the sort of thing a reasonable parser should be willing to forgive. ApE isn’t the only program to make that sort of mistake (or perhaps they’re working from an older technical spec), I’ve run into it in a couple of other places, so I do want to make importing from GenBank format more generous. (I have a rough version of it working now, but it’s pretty crude and misses a lot of features.)

Strict GenBank format with spacing is described at http://www.bio.net/bionet/mm/genbankb/2001-October/000103.html .

:)

Thanks for your speedy reply, I have found a workaround by playing with an APE genbank file until XPlasMap would accept it. It is below:

LOCUS pUASp 9551 bp mRNA linear VRT 29-MAR-2008
DEFINITION pUASp cloning vector.
ACCESSION
VERSION
KEYWORDS .
SOURCE Unknown
ORGANISM Unknown
Euk.
REFERENCE 1 (bases 1 to 9551)
AUTHORS none
CONSRTM
TITLE
JOURNAL
PUBMED
COMMENT none.

Below this are the ApE listed features which XPlasMap seems to find :)

I can just copy this into the top of ApE files I wish to view in XPlasMap. Thanks again for your help, now im off to make pretty plasmid maps… :)

Best wishes,

Paul

At the moment the short answer is “No”; sorry. I have had several requests for this and it’s on the list of things to do, but probably not for the next release.

One approach is that ApE exports to GenBank format, as I recall, and XPlasMap will import from GenBank. The bad news is that ApE’s GenBank export doesn’t quite fit the technical standard, and XPlasMap’s GenBank import only follows the strict standard, so it doesn’t recognize ApE’s files. I have written a more forgiving GenBank importer for the next version, so that may help some.

Love the software, was just wondering, is there an easy way for me to quickly edit my ApE files to view them in your program? Any help would be greatly appreciated!

Best wishes,

Paul Avery (PhD Student)