News Archive

Six new transcriptome datasets have been added to the Bactrocera dorsalis JBrowse. These data were contributed by Scott Geib, USDA-ARS, and include egg, pupae, larvae, male adult, unmated female adult and mated female adult. The original data are available through SRA: http://www.ncbi.nlm.nih.gov/bioproject/167923, and are published in BMC Genomics (doi:10.1186/1471-2164-15-942).

Jbrowse/Web Apollo updates:

Web Apollo has been updated to version 1.0.4. This includes several feature and stability updates. Please refer to the Web Apollo Git repository for a full list of updates
( https://github.com/GMOD/Apollo/blob/master/ChangeLog.md ).  One major change is the addition of the sequences page as an initial entry point to Web Apollo (e.g. https://apollo.nal.usda.gov/oncfas_training/sequences ).  The sequences page currently exists alongside selectTrack.jsp, and will eventually replace the selectTrack page in future versions of Web Apollo.

We would like to welcome three new species to the i5k Workspace@NAL!

More information for each of these organisms is available on their respective organism pages, and they are also available via BLAST and JBrowse. If you are interested in more information about these insects, please contact Scott Geib, community coordinator.

 

BLAST updates:

The color scheme for reporting HSPs now uses the static system by default. This system is based on the default NCBI system for reporting colors based on bit-score.

Viewing HSPs in Jbrowse/Web Apollo is now in color! Each HSP is colored based on the bitscore value, and uses the same color scale as the static color scale in the BLAST report. Right clicking on a feature to “View Details" now includes additional information at the HSP level based on the BLAST output. The HSPs are still draggable, and may be used as part of a feature annotation strategy. A big thanks to Han Lin for developing this feature!

There are several new user-provided tracks available for the Athalia rosae and Orussus abietinus JBrowse/Web Apollo instances.

Note that the tracks 'O. abietinus female cleaned reads, XY-plots' and 'O. abietinus female cleaned reads' replace the tracks 'Orussus abietinus female RNAseq cleaned unassembled reads, XY-Plot' and 'Orussus abietinus female RNAseq cleaned unassembled reads, alignments'. Similarly, the tracks 'O. abietinus male cleaned reads, XY-plots' and 'O. abietinus male cleaned reads' replace the tracks 'Orussus abietinus male RNAseq cleaned unassembled reads, XY-Plot' and 'Orussus abietinus male RNAseq cleaned unassembled reads, alignments'.

For Athalia rosae, the tracks 'AROS_ID05', 'AROS_ID06', 'AROS_ID07', and 'AROS_ID08' have been replaced with 'A. rosae female-1 raw reads', 'A. rosae female-2 raw reads', A. rosae male-2 raw reads', and A. rosae male-1 raw reads', respectively.

Dr. Alexie Papanicolaou has provided a set of predicted transposon domains for the Mediteranean fruit fly Ceratitis capitata.

You can view this new data in the C. capitata JBrowse/Web Apollo browser.

The i5K Workspace @NAL has had some major infrastructural updates, and now runs on Drupal 7 and Tripal 2.0. These changes should improve the speed and reliability of our website. Please let us know if you experience any problems.

We have been working with the group at Agripest to migrate two species into the i5k Workspace@NAL:
 - The Tobacco Hornworm, Manduca sexta (i5k.nal.usda.gov/Manduca_sexta)
 - The Hessian fly, Mayetiola destructor (i5k.nal.usda.gov/Mayetiola_destructor)

Dr. Felipe Barreto has provided a large number of evidence tracks for the Tigriopus californicus JBrowse/Web Apollo instance.