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Help Home > The Genome Browser > The Genome Viewer > Track Editing

Track and Model Editing

The Genome Viewer includes tools that allow you to create and edit new gAene models within specially allocated "User Model" tracks on the browser. "Track editing" features are available from three pop-up menus which appear when you click on features or exons within the viewer:

  1. You can create new models and exons from existing models by clicking on any (non User-Model) feature in the Genome viewer to bring up the Model Menu.
  2. You can examine and edit existing user models by clicking on a model in a User Models track to bring up the User Model Menu.
  3. You can edit user model exons by selecting Exon Menu from the User Model menu.

After creating a new gene model in the User model track, you can control other users' access to this model by Blocking or Releasing it. The model will appear in different colors based on its release status.

Note: Track editing features are only enabled within a given genome portal when you are logged in as a registered JGI user and have been granted annotation privileges for that genome.

  • To obtain annotation access, please send an email request to the JGI Annotation Group, including your JGI username (usually an e-mail address).

Creating new models and exons from existing models: The Model Menu.

Track editing generally begins by copying a gene model from a track on the browser into one of the User Model tracks. The new User Model is automatically assigned a new proteinID(LINK) and can be edited from within the User Model track.

To create a new model by copying an existing model, click on the model to bring up the Model Menu, shown below:

Gene Model pop-up menu

  • Feature web page will connect you to the Protein, Transcript or Alignment page for the selected feature.
  • Copy model to track> will make a new copy of this model in the selected user track.
  • The new model will appear in the chosen User Models track. The new model will be named by concatenating the first three characters of your user name and the original model name.
  • User models are color-coded on the track to indicate the current status.
  • Add exon to model will add this exon to the selected Model. Note that this menu option will only appear if you have clicked an individual Exon. you may have to zoom in on the model in order to easily select an exon.

Quick Tips

  • To view your new User models, click the track name (where you copied it) to expand the track.

Working with User-created models: The User Model Menu.

Once you have created a new model in a User Model track, click on this model to bring up User Model Menu :

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  • Transcript sequence brings you to a page displaying the nucleic acid sequence for this model or exon.
  • Protein sequence opens a page with the Amino acid sequence in FASTA format
  • 3-frame translation opens a page with the 3-frame Amino acid translation.
  • Zoom brower into> zooms and centers the browser on the model or one of its exons.
  • Copy model to track> copies this model to the selected track.
  • Create new model allows you to create a new ab initio gene model in this track.
  • Delete user model removes this model from the User Models track.
  • Change strand moves the model from the + to the - strand, or vise-versa.
  • Release User Model releases the model, making it available for other JGI users to view and edit.
  • Create new exon allows you to create a new ab initio exon in this model.
  • CDS coordinates allows you to change the start and end positions of this model.
  • Exon menu allows you to edit the exon structure of this model. This menu option is only available if you have clicked on an exon. Try using the Zoom browser into> option above to make it easier to select an exon.

Gene structure editing: The Exon Menu.

The exon menu allows you to alter, add, and remove exons to a gene model. To reach the Exon Menu, click on an exon within a model in a User Model track and select "Exon Menu" at the bottom of the pop-up.

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When you select Exon Menu, A drop-down menu and editing boxes appear as well as vertical lines that position the exon relative to the amino acid sequence under the scaffold. These vertical lines align with the outer edges of the amino acids at each end of the exon. At this point you can:

  1. Add Exon to model>: add this exon to another existing model on your track
  2. Merge exons>: merge the selected exon with upstream or downstream exons which will create one large exon without any intron sequence
  3. Delete user exon: delete the exon from the model entirely.
  4. Model menu. Return to the model menu.
  5. To edit the exon, enter new coordinates into the editing boxes, or extend or shrink the exon from either end 1 - 3 nucleotides at a time using the + and -. Click Save in any box to save your changes to the exon coordinates.

Quick Tips

  • To return to the drop-down menu for the model itself, without making any edits to the exon, click Model menu.
  • If you want to edit an existing model that was already released (colored green on the "User Models" track), click Block User Model to block community access to this model while you are editing.
  • To view the sequence code on the scaffold while editing an Exon or CDS, click the AA or NA buttons in the Browser Navigation Controls.
  • If you want to restore the coordinates for an Exon or CDS after editing, but before saving it, click Default in the menu.

To edit the CDS of a model:

  1. Click on the model you want to edit. A menu opens with the name of the model you selected.
  2. From the menu click CDS coordinates. A drop-down menu and editing boxes will appear as well as vertical lines that position the exon relative to the amino acid sequence below the scaffold. These vertical lines align with the outer edges of the amino acids at the beginning and end of the CDS. NOTE: If the CDS edge is out of the visible area the menu will not appear.
  3. To edit the CDS, enter the coordinates into the editing boxes, or extend or shrink the CDS from either end 1 - 3 nucleotides at a time using the + and -. Click Save in any box to save your changes to the CDS coordinates.

When you have finished editing a model and are ready to release it to the community, click Release User Model.

Create an Ab Initio Model or Exon

If there is no model predicted but there is EST data, protein BLASTx hits, or a user generated BLAST/BLAT alignment at the locus of interest, then:

  1. Expand the EST, BLASTx or User BLAST/BLAT track and click on a specific EST. protein or BLAST/BLAT alignment.
  2. From the model menu select Copy model to track and choose the "User model" track.
  3. Follow the directions under Edit Model on the User Track

If there is no predicted model and there are no EST or protein alignments at the locus of interest, first determine whether the "User Models" track contains any models. If there are models present:

  1. Click on any model in the "User Models" track and select Create new model.
  2. A new window will appear asking for a Model name and the strand on which you would like to create your model. Enter this information and select Save. The browser will refresh and an empty track will appear. On the left-hand side of the empty track a label will appear containing the first three letters of your user name followed by the name of your new model.
  3. At this point you can build the new model, exon by exon. To create the first exon of your new model, click on the empty track and select Create new exon. A new window will appear asking for an Exon start and an Exon end. In this window you must enter the genomic start and stop coordinates for your new exon. Click save. The browser will refresh and your new exon will appear in the "User Models" track.
  4. To create a multi-exon model, click on the exon you just created and, same as in step 3, enter the genomic start and stop coordinates in the new window for the next exon. These two new exons will automatically merge to create a multi-exon gene model.
  5. When you are finished creating new exons, click on the new model and select Release User Model. Protein analysis is automatically run on released, user created models and a protein page will be generated. Once the analysis is complete---which can take from 5 minutes to an hour--you can start annotating your new model.

If there are no models present in the User model track:

  1. Condense the "User Models" track.
  2. Click on the empty space below the "User Models" label on the browser. Select Create new model.
  3. A new window will appear asking for a Model name and the strand on which you would like to create your model. Enter this information and select save. The browser will refresh. Click on the "User Models" label to expand the track or on the + (plus sign) at the far left side of the track. An empty track will appear. On the left-hand side of the empty track a label will appear containing the first three letters of your user name followed by the name of your new model.
  4. At this point you can build the new model, exon by exon. To create the first exon of your new model click on the empty track and select Create new exon. A new window will appear asking for an Exon start and an Exon end. In this window you must enter the genomic start and stop coordinates for your new exon. Click save. The browser will refresh and your new exon will appear in the "User Models" track.
  5. To create a multi-exon new model click on the exon you just created and as in step 3 enter the genomic start and stop coordinates in the new window for the next exon. These two new exons will automatically merge to create a multi-exon gene model.
  6. When you are finished creating new exons, click on the new model and select Release User Model. Protein analysis is automatically run on released, user created models and a protein page will be generated. Once the analysis is complete---which can take from 5 minutes to an hour--you can start annotating your new model.

Release and Block Models

To release a model:

  • Once you have finished editing a model, click on the model and select Release User Model. The model color will change from red to green, indicating that it is now available to edit by all users.

The release method also runs several genome model integrity tests:

  • Check if CDS length is divided by 3
  • If transcript start <= CDS Start
  • If transcript end >= CDS end
  • If CDS start or end is in model intronic space.

If there are no errors you can proceed with the release.

The model color will change from red to green indicating that it is now available to be edited by all users. Released models then become publicly visible.

To block a model:

  • Blocking a user model ensures that only one person can edit a model at a time. To use this feature while editing an existing model on the User Track, click on the model and select "Block User Model". The model color will change from green to red, indicating that it is now blocked from editing by all users.

Explanation of Model Coloring

Green:

  • The model is currently released. Automated protein analysis is performed on these models. You can access this analysis on the model's protein web page.

Blue:

  • The model was just copied and has not been edited. The model is currently blocked and can be modified only by the user who copied it to the User Models track.

Red:

  • The model has been edited by the user and has not been released. The model is currently blocked and can be modified only by the user who copied it to the User Models track.