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sequenceserver -mwill now automatically detect older V4 databases, and those created without the
makeblastdb, and offer to rebuild them. This works even if you deleted the original FASTA files. Database titles are preserved when rebuilding, however, taxonomy information in the database is unfortunately not preserved.
- BLASTing a mix of older V4 and newer V5 databases causes error. SequenceServer now catches and informs the user of this error. Thanks to Massimiliano babbucci for reporting this issue.
- The list of databases in the search form should be alphabetically sorted. This behaviour was lost in the rewrite leading to version 2.0 and has now been fixed. Thanks to Loraine Guéguen for reporting the issue.
- Improve regular expression used to detect multi-part databases, so that databases that aren't multi-part are recognised and displayed in the interface (#465). Issue reported and fixed by Loraine Brillet-Guéguen.
- On sub-URI deployments, back-button would result in no databases to be displayed in the search form (#462). Fixed that. Thanks to Xiang Zhang for reporting the issue and testing the fix.
- A programming error prevented databases from being deselected when you go back to the search form after submitting a query. That's now fixed. Thanks to Norman Johnson for reporting the issue.
- Database creation step could skip FASTA files containing too many Ns at the beginning of the file. Fixed that. Thanks to Michał T. Lorenc for reporting the issue.
- During the initial setup, SequenceServer would print the message 'config file not found' multiple times. Fixed that.
- Results page would fail to load completely if the submitted queries resulted in no hits. Fixed that.
- Give users an option to sign up for release and other important announcements during the initial setup.
- Highlight the use of non-default parameters by changing the background of advanced parameters field to yellow when filled.
- Include SequenceServer version and a link to our paper in the search summary at the top of the results page.
- Fix BLAST version comparison to check compatibility, so that 1.0 series can work with BLAST 2.10.0 (issue raised by Takekazu KUNIEDA)
- Point to our MBE paper instead of biorxiv when SequenceServer is terminated
Summary of changes since version 1.0:
- Support for BLAST 2.10.0 and the new BLAST database format.
- Results now open in a new page. You can share the link with colleagues or
bookmark the page and return to it at a later date. Results are saved for 30 days.
- We have integrated three new visualisations that facilitate interpretation of BLAST results:
Length distribution (histogram) of all hits of a query. This is inspired from our work with GeneValidator (https://academic.oup.com/bioinformatics/article/32/10/1559/1742817) and can, for example, help quality-assessment of gene predictions.
Kablammo visualisation (https://academic.oup.com/bioinformatics/article/31/8/1305/212772) for each query-hit pair indicates clearly which parts of the query match which part of the hits.
Circos-style plot of all queries and their top hits. This is similar to the circoletto tool (https://academic.oup.com/bioinformatics/article/26/20/2620/194655) but for a small number of queries. For example, it can help visually testing for conserved synteny or gene duplication.
- We provide a command-line mechanism for importing a BLAST XML file and visualising it in SequenceServer. This works for DIAMOND as well. We do not yet provide a graphical user interface for this.
- The 30 hit limit for FASTA download has been removed. In addition, you can now download
raw pairwise alignments.
- Better support for long-running BLAST searches, for rendering large BLAST results, for
integrating as part of other websites.
- Improved error handling, security enhancements, and a new look.
Changes since the last beta release:
- Upgraded to BLAST 2.10.0
- We have improved the ability to render "large BLAST results" (thousands of hits). We expect
this to facilitate visualisation of large gene and repeat families.
- Form data is now restored when you press back-button in the browser from the results page.
- We have a logo and a new look!
New features since 1.1.0-beta12
- Update to BLAST+ 2.9.0
- Ability to import BLAST results in XML format from DIAMOND and BLAST versions 2.2.30 - 2.9.0
- Ability to pre-populate textarea with server-sent query sequences (thanks to Richard Challis for feature suggestion and initial implementation)
- On startup, sequenceserver now tries to determine the ip and the hostname of the server and prints two URLs that may be suitable for sharing with colleagues
- Recognise PFAM and RFAM hit/subject ids and include a link to the hits PFAM or RFAM page (credit: Tomas Pluskal)
Bug fixes and refinements
- In a suburi deployment (e.g., antgenomes.org/blast), take suburi into account when constructing url for the results page (thanks to Guy Leonard for reporting the issue)
- Use more specific regex for determining non -parse_seqids databases. Otherwise, presence of 'gnl|' in sequence ids would disable sequence retrieval (thanks to Josh Goodman for reporting the issue)
- Length of query and hit sequences are now easily accessible in the report page. This is included in the query and hit header, on the right hand side, in a gray font
- Restored the ability to fold and un-fold individual hits (credit: Josh Goodman)
- Removed .00 from decimal numbers (i.e., 100.00% is now shown as 100%)
- Fixed vertical alignment of links and buttons provided for each hit
- Removed trailing comma in HSP statistics line for BLASTP
- Properly wrap text in the summary overview on top
- Sequence lengths were erroneously downscaled by 100. Fixed that
- Formatting of e-value and identities in the tooltips was inconsistent with the rest of the report. Fixed that
- Ribbons had no colour for the specific case of 1 query and 2 hits. Fixed that
- Filter out queries with no hits before drawing the visualisation
- Change to more meaningful title 'Chord diagram: queries and their top hits’
Length distribution of all hits for each query:
- When query and database are in different sequence space (DNA or protein), normalise query length to match database space (#409)
- Reduced the number of ticks in the y-axis otherwise the ticks looked too “squeezed up” when there were too many hits
- Round up the number of ticks on x-axis so that the scale ends consistently in a major or a minor tick
Code quality improvements
- Fixed many of the warning messages generated by React in browser console
- Expanded test coverage and improved automated testing