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Citation

Please cite:
Robb SM, Gotting K, Ross E, Sánchez Alvarado A., SmedGD 2.0: The Schmidtea mediterranea genome database., Genesis 2015 Jul [Epub ahead of print]

Version

This is SmedGD 2.0

Smed Unigene Help

Definition

  • Smed Unigenes are amino acid sequences that represent a cluster of similar transcript sequences. This amino acid sequence enables a series of protein motif predictions to be calculated and displayed in the Smed Unigene GBrowse instance and in the Smed Unigene Gene Page. Tools have been generated to download the amino acid sequence and the clustered transcript nucleotide sequences.
  • Smed Unigenes have identifiers that begin with ‘SMU’.
  • Every Smed Unigene has a gene page that can be found by performing a Smed Unigene protein domain or GO term search or by selecting ‘SmedGD Unigene’ from the Pop up balloon on any of the protein homology tracks in the Smed Unigene Browser.

Putative Function

  • The putative function of each Smed Unigene is determined bioinformatically. Each of the associated transcripts have been used to search Swissprot and enSEMBL databases. All of the hit descriptions (for each Smed Unigene associated transcript) is examined for common phrases (more than one word) across transcripts. The longest and most common phrase that appears in more than one transcript hit descriptions is used as the putative function. “Cannot be determined” indicates that no common phrase could be found in more than one transcript

Multiple Assemblies

 

  • Multiple Genome Assemblies as well as a Smed Unigene browser are available for viewing and search with GBrowse. Links can be found in the top menu from within the “GBrowse” tab. Links to each Browser can also be found within any of the Browsers from the dropdown menu entitled “Data Source”.Additionally each Browser can be accessed from these links:

Gbrowse Help

General Help

  • See GBrowse Help Page Here

User Accounts

  • Create an account to save information you would like to return to at a later date, such as Snapshots

Bookmark this

  • Find the ‘Bookmark this’ function in the Gbrowse File menu.
  • This function generates a URL which can then be bookmarked with your Web Browser.
  • This URL contains information about the reference sequence and tracks in your current view

Snapshots

  • To save the current browser view for your future reviewing, including the specific reference sequence and track selection simply select ‘Save Snapshot’
  • To save the current browser view for others first select ‘Bookmark this’ in the ‘File’ menu, then select ‘Save Snapshot’
  • Snapshots can be retrieved and sent to other from the ‘Snapshot’ tab

Custom Tracks

  • Upload your own track from a file or URL.
  • This track can be in a variety of formats, gff3, bed, wig, etc.
  • See the custom track help page for information about file formats
  • Save your custom track as ‘Casual’ and share the link with others
  • Save track as ‘Private’ and only you can view it
  • Save track as ‘Public’ and it will appear in the ‘Community Tracks’ tab for everyone to see.
  • Read this manuscript written by Lincoln Stein explaining how to share Next-Gen seq data, “Using GBrowse 2.0 to visualize and share next-generation sequence data

Contact Us

planosphere@stowers.org