News Archive

We are pleased to release the i5k Workspace, version 2.0! This newest release features a fully updated user-interface that we designed for easier navigation for new and recurrent users. If you have bookmarked your favorite links within the i5k Workspace - all of our tools and pages are still available under the same URLs. We hope that you enjoy the new interface, and as always welcome your feedback and suggestions!

We have several new datasets available for viewing on our genome browsers:

Diaphorina citri: Several new RNA-Seq datasets are available. There are also new mapped results from proteomics data generated by John Ramsey, Surya Saha and Michelle Cilia.

Hyallela azteca: Helen Poynton's group has mapped results from some recent RNA-Seq experiments to the genome.

Blatella germanica: Kim Walden has aligned published RNA-Seq data to the genome; you can view the tracks here. Additionally, new RNA-Seq data from NCSU are also available for viewing.

Frankliniella occidentalis: Dorith Rotenburg's group has generated a new transcriptome assembly with cufflinks.

 We have a number1 of new datasets visualized on several genome browsers:

- Two new transcriptomes mapped to the Frankliniella occidentalis genome
- New RNA-Seq data for Bactrocera dorsalis
- new OGS uploaded for Anoplophora glabripennis
- Transposable element predictions and miRNA predictions in Leptinotarsa decemlineata
- RNA-Seq and transcriptome data from the 1Kite project contributed to Catajapyx aquilonaris
 

We have re-structured our data downloads section (https://i5k.nal.usda.gov/data; or, for a nicer graphical user interface, https://i5k.nal.usda.gov/content/data-downloads). We hope that the new structure is easier to navigate. Please note that if you have bookmarked certain datasets before, that thse links are likely now broken.

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!