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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> Plasmid maps and qualifiers https://forum.ugene.net/forum/YaBB.pl?num=1338554264 Message started by dustman on Jun 1^st, 2012 at 7:37pm

Title: Plasmid maps and qualifiers
Post by dustman on Jun 1^st, 2012 at 7:37pm

I have a mix of GenBank and FASTA files depicting plasmids, primers, etc. So far I got couple of problems I can't figure out how to solve :(

1. In graphical plasmid view all qualifiers are shown under their generic names, i.e. 'promoter', 'rep_origin' and so on. It would be nice if labels were used for markings instead, i.e. 'CMV promoter' or 'pUC origin', or it could be done using couple of mouse clicks.

2. Automated annotation of FASTA files when asked for, like it done in PlasMapper... or at least possibility to create a local database based on annotated sequences...

Help would be really appreciated :)

Title: Re: Plasmid maps and qualifiers
Post by Agu on Jun 1^st, 2012 at 8:53pm

Hi, dustman.

1. You have to indicate the name of the qualifier that you want to be displayed using the highlighting panel on the right. Check this:
http://genome.unipro.ru/documentation/manual/sequence_view/annotations_manipulations/highlight_annotations.html

2. I don't get it. Can you be more specific? FASTA files contain only sequence, so is not possible by definition. You could save a copy as genbank and then annotate them. Also, you can make a workflow that reads the fasta file, searches for all the features you want and then save them as genbank files.

Title: Re: Plasmid maps and qualifiers
Post by dustman on Jun 3^rd, 2012 at 4:19am

Thanks Agu, no.1 worked fine.

As for FASTA.. Many elements in plasmids are quite common, like CMV or SV40 promoters, pUC origin, Amp(R) or Kan(R)/Neo(R) and so on. If database of such elements exists and is checked against for a FASTA sequence, manual annotation of certain elements can be avoided. Most likely CDSs and Kozak/SD sequence must be checked manually, but initial automation would be appreciated. Don't know if it makes more sense now.

Title: Re: Plasmid maps and qualifiers
Post by Konstantin Okonechnikov on Jun 5^th, 2012 at 2:23am

Quote:

As for FASTA.. Many elements in plasmids are quite common, like CMV or SV40 promoters, pUC origin, Amp(R) or Kan(R)/Neo(R) and so on. If database of such elements exists and is checked against for a FASTA sequence, manual annotation of certain elements can be avoided. Most likely CDSs and Kozak/SD sequence must be checked manually, but initial automation would be appreciated. Don't know if it makes more sense now.

We have the automatic annotation feature similar to PlasmidMapper planned for 1.12:
https://ugene.unipro.ru/tracker/browse/UGENE-125

When this feature is implemented, it will be possible to provide predefined annotations bases, for example common plasmid features etc.