When it comes to creating data, we have never been so productive. But the more we have, the harder it is to interpret and share.
CrustyBase aims to unite our scientific efforts by serving as a community database for crustacean transcriptome data. Find new datasets with the Data Browser, then use the BLAST tool to find specific sequences within them.
CrustyBase started with a great dataset that we really wanted to share.
By utilizing the unique life history of the rock lobster, we generated a transcriptome series providing novel insights into arthropod development.
If you have access to crustacean transcriptomes, why not share them with the world?
We allow two levels of data access, so you can even share data without exposing the raw data needed for publishing. We hope that this will enable more collaboration and prevent researchers from missing out on data that would have enabled discoveries.
Import dataPatched BLAST error
8th July 2021
Some CB users may have experienced an error running some BLAST searches - this error occurred when the requesed BLAST databases shared a common sequence identifier. Unfortunately this is a feature of the BLAST+ blastdb_aliastool that we use to concatenate BLAST databases on-the-fly. We have applied a temporary patch to the CB database which prevents this error from occuring - you may notice that contig IDs on some datasets are now appended with "_2", "_3" etc. We plan to update the BLAST tool soon with a long-term fix for this issue.
Upgraded BLAST toolkit
8th July 2021
Our BLAST toolkit has been upgraded to version 2.11.0+. All BLAST databases have been rebuilt for compatability.
BLAST result interface improved
9th May 2021
The BLAST results interface now displays a "Feature legend" when you mouse-over the expression chart, which describes X-axis labels. We're also aware that the BLAST result's "expanded" view does not work well on smaller screens, so we made some small adjustments which should hopefully improve the interface on these devices. There's a lot going on here, so it can be a bit of a challenge to fit it all in!
Missing domain/proteins error
8th May 2021
Earlier this week, the CrustyBase server reported an error with the new "Panulirus argus" dataset, where protein and domain information appeared to be missing. We checked out this issue yesterday and found that the NCBI "makeblastdb" tool (which builds our BLAST databases) was re-formatting contig IDs to uppercase in an arbitrary fashion, leading to mismatches against the database. We have notified the NCBI that this may be a bug in the BLAST+ toolkit, but have added a temporary fix until this has been resolved.
Import pipeline bug fix
28th March 2021
A user reported cases where the predicted proteins (downloaded proteins and predicted domains) for some transcripts were in the wrong frame. We checked out this issue and found that the CrustyBase import pipeline (where new datasets are processed) was calling TransDecoder without the "--single_best_orf " flag. We updated the pipeline to fix this, ensuring that all predicted ORFs are full-length. We then repeated the predictions for all existing datasets, which have now been updated in the database. Thanks to this user for reporting the issue - if you come across anything that looks like a bug or error, do let us know so that we have a chance to fix it!
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