News and Announcements
Attention: Jul 27, 2017 TRDB Maintenance is complete.
Attention: Jul 26, 2017 TRDB will be down for maintenance tomorrow, Jul 27, 2017 from 8:00am EDT to 12:00pm EDT. Use this link to convert this time to your local time zone.
Attention: there are 2 scheduled maintenance tasks in TRDB. One runs daily at 10:00 PM EST and lasts about 15 minutes. Second one runs weekly on Saturday 12:00AM EST and lasts about 2 hours. It is not recommended that you start any jobs right before the Saturday maintenance task.
Attention: As of August 26th, 2005, TRDB is using TRF version 4.0. The quality and the number of repeats found improved with this new version. All public genomes will also be processed with the new version of TRF. The standalone versions of TRF 4.0 is now available here.
Our public genome data is processed using TRF parameters 2,-7,-7,50. We also have processed some genomes using 2,-5,-5,20. These are only available as compressed plain text files here.
Data in TRDB may differ slightly from other sources that use TRF, as we run a special function on all repeats to find better patterns.
- added redundancy tool to TRDB
- better faster clustering for TRDB
- registration changed to automatically send pass reminder if user already exists but registers for different database
- changed batch processing to not get stuck if all jobs are stuck
- changed .gff parser to work faster (atof func too slow)
- added download from browsing repeats feature
- fixed download problem where long set names caused file extension to be lost
- added more places where an email is prompted for the guest account
- downloading clusters now uses the same interface as downloading sets
- selected download columns now persist between sessions
- repeat array sequence is now referred to as "array sequence" in the download, no longer as "subsequence"
- "USE MASTER" option in multalignment is no longer the default, that option seems to occasionally produce incorrect alignments where entire rows are incorrectly shifted, to be addressed in the future bug fixes
- Now image headers are produced for saving these resources: flank comparison, repeat alignment, mult alingment, browser, distributions, history and the cluster search tool output
- added browsetables for public sets to speed up browsing
- added reports default save as project box
- now displaying organism for set information pages
- Fixed sequence download bug which was cutting off sequences in multi-fasta format.
- Some changes to default clustering parameters
- Added a button to TRDB/IRDB to quickly check a repeat against the Repeat Masker database.
- Added tool to search for exact patterns
- Added tool to import sets
- Added an action to download a cluster (sequences only in correct direction). Note, if saving as a set, direction is lost.
- now distribution table and clusters table can be added to a report
- added Set Comparison tool (TRDB only so far) to compare two sets ran at different parameters or with a different algorithm version
- changes to IRDB reflecting IRF3.03 changes as extra fields and changed process form
- changed copying/merging/saving/clustering/tools on sets to preserve comment,sub-pattern fields, polymorphism prediction tools, etc.
- sub-pattern detection tool added (TRDB only)
- new sequence selection dialog implmented
- support for GT match and Mirror repeats options programmed in (IRDB only)
- added PRINTER FRIENDLY COLORS button to the repeat alignment page
- modified TRDB to display possible pattern fragments in the flanks when flanks are selected on the repeat alignment page
- modified IRDB to display flank alignments when flanks are selected on the repeat alignment page
- clustering revamped and moved to the computation cluster :)
- function for managing multiple remote jobs from the same client added
- modified IRDB GFF export file to include the UCSC custom track header, also it is now made of 2 parts (left and right arms) and not a continuous blob as before
- added arm join tool (IRDB Only)
- added Multiple Sequence Summary display
- added removing yourself from a project as well as transferring ownership of a project
- now it is possible to delete a project and all its content in the same operation
- project and partition group are preserved when jumping around the pages
- when going to the browser from a particular repeat, that repeat is now surrounded by a red square
- also it is possible to switch between other sets that repeat is part of while staying on the same sequence position
- added save to report feature to flankcomp output
- now when saving a set or report, it is possible to create a new project on the fly
- process id of each transaction is now saved in the logs so it is easier to track run away processes
- fixed a few problems with the GU library (v1.05 now) (affects distributions graphs)
- better statistics
- added a guest user type
- added a gapper tool to IRDB
- implemented multiple set merge
- added scatter plot to the distributions page using our new graph library
- fixed the "view history" bug which caused errors in big displays due to pallete running out of colors
- added preregister page to collect information about users before they register
- implemented automatic GENBANK sequence pull
- added a "veiw scheduler statistics" administrative tool
- fixed a bug that incorrectly displayed repeat count when saving "as cluster" in IRDB.
- fixed a bug that prevented adding records from a cluster to a report
- added a comment field on the repeats table and an index on the repeats table to speed up some queries
- created a distributed version of the program (we now have a 4 node cluster to take advantage of that). Right now we
only use it for sequence processing, but soon other tasks as "clustering" will follow.
- added a new "Collaborator" user role that has some extended properties
- created a joined preapproval table which is now a part of a centralized security system
- IRDB no longer keeps the loops saved. Loops and flanks can still be accessed if the original source sequence is not deleted. There is no visible difference for the user.
- browser, distribution and popups now do not jump away from the data after refreshing (except that it cause NS to freeze,
to it is only available for IE)
- found a bug in the browser that wasn't letting the user pick the zoom level in some cases
- redundancy tool (IRDB only)
- new browser zooming selection options
- added multiple alignment (IRDB)
- all annotations on the browser now have a link to a more detailed popup (unless the density of annotations becomes too high)
- fixed the browser stacking so it no longer produces huge unbalanced stacks
- added the "compare flanks" tool (TRDB only) as well as an alignments options to the account to be used by it
- added the Transcriptions Binding Factors Prediction tool (TRDB only)
- added the flanking display to repeat view
- modified the sequence download page so that masking and range select options are available
- added display of annotations to the browser
- some alignment corrections for MREPS found repeats and a new field called "Sensor" added (TRDB only)
- completed DAS client and used it to annotate our public sequences. The client is now automatically run once a week.
- a new sensor for finding exact tandem repeats of unlimited size (MREPS) added to TRDB
- added "composable FASTA" set download option which lets the user to create a custom string from available DNA strings
- fixed a memory bug in image distributions
- fixed a bug in TRDB "copy labels" tool which caused copies to be mislabeled (TRDB only)
- added the DAS (annotation source) information to the sequence modify page (administrative only)
- created this update file and placed a link to it on the about page
- added REPORTS feature
- added positional view (browser) for repeats available from the distributions page)
- spelling error fix on filter page ("greater than or equal to")
- changed text on the download and primers forms for line termination to be more understandable
- the process of uploading a sequence is now simplified (organism is now optional and a default name is provided for the sequence)
- Fixed the bug in IRDB where loops where saved with some added garbage at the end. Run a script on the database to update affected rows.
- Added flanking sequences to the set download (before you could only get them from the primers page in TRDB)
- added a button to the "label copies" tool to download the copy definition FASTA file (TRDB only)
- Fixed "FASTA" set download (TRDB only)
- added textual pattern and sequence to the repeat viewer (TRDB only)
- Major release. A common webcore is established (LBIwebbase) and 2 child databases (TRDB and IRDB.) Update file not yet kept.
- First version. Update file not yet kept.