Lotus Base Blog
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Posts
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20 Apr 2020 L. japonicus Gifu v1.2 genome
Terry Mun
L. japonicus Gifu v1.2 genome has been publicly released. It is now accessible via the Genome Browser, as well as other tools on the sites, such as the Expression Atlas...
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21 Nov 2018 Post-mortem on downtime experienced by BLAST-related tools
Terry Mun
Over the course of the weekend of November 17–18 of 2018 and the subsequent working week that follows, all BLAST-related tools on Lotus Base became inaccessible. The affected modules were:...
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12 Dec 2016 GateKeeper—Migrating away from IP-based controlled access
Terry Mun
We are announcing in a change in user access to controlled, internal data available to CARB members with immediate effect. Traditionally, we have been offering access to CARB members based...
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28 Nov 2016 Using InterProScan like a pro
Terry Mun
Biologists are often challenged with this question when working with proteins. This article enunciates the process of using InterPro(Scan) to predict protein domain and function. Predicting protein domain(s) and therefore...
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26 Aug 2016 Introducing ExpAt, the Lotus japonicus Expression Atlas
Terry Mun
Expression data from the model legume Lotus japonicus, while publicly available through other online resources, face a fragmented landscape that lacks accessibility and options for analysis and visualisation. Here we...
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24 Aug 2016 Mapping transcripts across Lotus genome versions
Terry Mun
The availability of various versions of the L. japonicus genome, while proving to be an important resource in legume research, makes it difficult for users to map annotated genes and/or...
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05 Mar 2016 Redesigned LORE1 search form, and pan-version TREX searches
Terry Mun
Lotus Base was originally conceived as a very simple web interface for the searching for, and ordering of, LORE1 lines, but over the years it gradually evolved into a fully-fledged...
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01 Mar 2016 JBrowse updated to v1.12.0
Terry Mun
We have successfully upgraded our JBrowse installation, used to power visualization of the L. japonicus genome, to version 1.12.0.
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27 Jan 2016 Lotus Base Soft Launch
Terry Mun
After in a few years of continuous development, we are soft-launching Lotus Base, an online resource platform for the model legume Lotus japonicus.
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13 Aug 2015 Change in v3.0 gene nomenclature
Terry Mun
We are updating gene nomenclatures in Lotus japonicus to make gene names compatible with future genome versions.
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22 May 2014 Retirement of LORE1 flanking sequences BLAST database
Terry Mun
After much deliberation, we have decided to retire the LORE1 flanking sequences database because it does not contain LORE1 original reads, but only sequences that were extracted from the reference...
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18 Nov 2013 New LORE1 lines available and BLAST update
Terry Mun
LORE1 lines from batches 08, 09 and 10 are now available for searching. A new BLAST database has also been made available in light of the availability of new LORE1...
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17 Oct 2013 TREX Tool
Terry Mun
The Transcript Explorer (TREX) tool is now available, and allows fetching of genome coordinates of Lotus transcripts based on their IDs.
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01 Oct 2013 LORE1 database update
Terry Mun
The LORE1 databases (both v2.5 and v3.0) have undergone massive restructuring, in line with efforts to atomize database entries and normalize all databases. New lines have been added to the...
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17 May 2013 New BLAST databases available
Terry Mun
The Lotus BLAST has been updated with three additional databases: Lotus japonicus MG20 v3.0 cDNA Lotus japonicus MG20 v3.0 CDS Lotus japonicus v3.0 Proteins
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17 May 2013 Lotus genome browser
Terry Mun
The Lotus genome browser is now ready to use. We will keep updating JBrowse to the latest version.
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10 Apr 2013 Adjusting BLAST algorithm for short sequences
Terry Mun
If your BLAST queries are short (e.g. miRNA sequences), you might want to adjust the BLAST algorithm to get optimum results. Short sequences that are less than 20 bases will...