Monica Munoz-Torres (Annotation question)

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Monica Munoz-Torres (Annotation question)

Niederwanger, Michael

Hello,

 

Some time ago I had (and still have) issues annotating a gene in Apollo but I have to finish it soon. It’s all there, but I am simply not able to annotate  it.

 

@Monica Munoz-Torres: Kindly you offered help with finalizing my annotation. I wrote an email to you approx.. 2 weeks ago with a question, but I think you did not receive it since I sent it to: Monica Munoz-Torres [hidden email] directly. I also sent one to Scott Emrich.

I don’t know if that works or if I need a different email address.

 

To remember what I am talking about

Part of my email:

 

In the mails from the Apollo list was the suggestion to simply drag the BLAT results into the User created annotations area within Apollo. However this does not work, or I’m too stupid. Also there was a suggestion that every alignment file can be used as a template. I used clustal w for alignments, but how can I get a file format out of this which can be opened in Apollo? Or do I need different alignment program? I couldn’t drag or use the alignment files from vectorbase as well.

I’m at a loss what to do.

If possible I would like to send to you a partial sequence (or full sequence) of the gene in question (Word file or FASTA), from which I would be able to continue annotating. When using this for a BLAT search in Apollo it gives you 100% match and shows nicely the regions within Apollo (LGUN_random_Scaffold…). And this is where it ends (where I end). I am not able to continue. Can you help me to convert this sequence in any format that can be recognized by Apollo? Or how would you do it?

 

It would be awesome if you or someone could help me with that,

 

Kind  Regards

Michael Niederwanger

 

 

 

 

 





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Re: Monica Munoz-Torres (Annotation question)

Colin
Hi Michael

Thanks for letting us know about the need for this. I think some groups have developed some integration of BLAT or BLAST into their pipelines for this purpose but Web Apollo doesn't have a ready-made solution yet.

One example is the i5K project created a great web portal for loading BLAST tracks into Web Apollo! See their tutorial, they may also be available for comment.



On the other hand, we can also talk with Monica Munoz-Torres to get you more immediate help, because there are definitely workarounds for this if you need to just "get the job done"

For example, you can perform a BLAST/BLAT search locally and convert those results to GFF3 and load those into the genome browser. That is probably the easiest workaround currently!


Hope that helps!
-Colin

On Fri, Aug 21, 2015 at 5:02 AM, Niederwanger, Michael <[hidden email]> wrote:

Hello,

 

Some time ago I had (and still have) issues annotating a gene in Apollo but I have to finish it soon. It’s all there, but I am simply not able to annotate  it.

 

@Monica Munoz-Torres: Kindly you offered help with finalizing my annotation. I wrote an email to you approx.. 2 weeks ago with a question, but I think you did not receive it since I sent it to: Monica Munoz-Torres [hidden email] directly. I also sent one to Scott Emrich.

I don’t know if that works or if I need a different email address.

 

To remember what I am talking about

Part of my email:

 

In the mails from the Apollo list was the suggestion to simply drag the BLAT results into the User created annotations area within Apollo. However this does not work, or I’m too stupid. Also there was a suggestion that every alignment file can be used as a template. I used clustal w for alignments, but how can I get a file format out of this which can be opened in Apollo? Or do I need different alignment program? I couldn’t drag or use the alignment files from vectorbase as well.

I’m at a loss what to do.

If possible I would like to send to you a partial sequence (or full sequence) of the gene in question (Word file or FASTA), from which I would be able to continue annotating. When using this for a BLAT search in Apollo it gives you 100% match and shows nicely the regions within Apollo (LGUN_random_Scaffold…). And this is where it ends (where I end). I am not able to continue. Can you help me to convert this sequence in any format that can be recognized by Apollo? Or how would you do it?

 

It would be awesome if you or someone could help me with that,

 

Kind  Regards

Michael Niederwanger

 

 

 

 

 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.