Dear Bhoomi, Unfortunately BOGAS will not be a suitable choice at this stage in your project. BOGAS is intended to work on genomes that already have an initial automatic gene prediction, it is not capable to do de novo annotation of genomes. I'm afraid that you will not find many 'plug and play' pipelines on the internet. That is because it takes time and effort to adapt existing pipelines to new organisms. Usually people start of with an existing pipeline/software (eg. AUGUSTUS, EuGene, FgenesH, ...) for gene prediction and than adapt it to the new species or they team-up with labs like ours (working with EuGene) or the lab of mario stanke ( the augustus people ) . If you insists on online approaches I think that the tools I mentioned before all have an online instance (on our website you can find EuGene for example) but they will all only deliver basic functinoality. I hope this helps. best regards, lieven ----- Original Message -----
From: "Bhoomi Bhatt" <bhoomi_1789@yahoo.com> To: "Lieven Sterck" <liste@psb.vib-ugent.be> Sent: Tuesday, March 20, 2012 6:32:36 AM Subject: Re: [Beg-bogas] request for user account
Dear curator, I am right now working on saccharomyces cerevisiae just as an example otherwise i had to work on encephalitizoon cuniculi. I have to do denovo annotation of fungal organism for which i have to use pipelines and i am not able to find web-based pipeline. Can u please guide me.
--- On Mon, 3/19/12, Lieven Sterck <liste@psb.vib-ugent.be> wrote:
From: Lieven Sterck <liste@psb.vib-ugent.be>
Subject: Re: [Beg-bogas] request for user account
To: "Bhoomi Bhatt" <bhoomi_1789@yahoo.com>
Cc: beg-bogas@psb.vib-ugent.be
Date: Monday, March 19, 2012, 3:08 AM
Dear Bhoomi,
thank you for your interest in our work.
unfortunately it is not possible to grant you access to the whole system, we have to do it genome-based. Can you therefore specify to which species you would like access to and perhaps also your particular interest for it.
I must also add that getting access while only add the possibility to edit gene-annotations, there is no additional info nor extra tools for registered users.
sincerely,
the bogas-team
From: "Bhoomi Bhatt" <bhoomi_1789@yahoo.com>
To: beg-bogas@psb.vib-ugent.be
Sent: Monday, March 19, 2012 7:02:06 AM
Subject: [Beg-bogas] request for user account
Respected curator,
I am Bhoomi Bhatt and I am working on fungal gene annotation. I would like to request for a user account for your web service.
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--
==============================================================
Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, UGent
Bioinformatics and Evolutionary Genomics Division
Technologiepark 927, B-9052 Gent, Belgium
Email: lieven.sterck@psb.vib-ugent.be
Website: http://bioinformatics.psb.ugent.be
==============================================================
"Facts are meaningless. You could use facts to prove anything
that's even remotely true" - H. Simpson
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson