Table 7. Comparison of features available on extant legume resources and Lotus Base.
| Legume Information System1 75 | Lotus japonicus2 or Medicago truncatula3 Gene Expression Atlas (Lj/MtGEA)10,98,99 | Kazusa DNA Research Institute4 9 | Medicago truncatula Genome Project5 74 | SoyBase6 73 | Lotus Base7 (this work) | |
|---|---|---|---|---|---|---|
| Species | 21 | 1; L. japonicus or M. truncatula | 1; L. japonicus | 1; M. truncatula | 1; G. max | 1; L. japonicus |
| Genome browser | Yes; GBrowse100 and JBrowse12 | Yes; for MtGEA only (available as external link) | Yes; GBrowse | Yes; JBrowse | Yes; GBrowse | Yes; JBrowse |
| Genetic map | No | No | Yes | Yes | Yes | No |
| Gene ontology | Yes | No | Yes | Yes | Yes | No |
| Data mining | Partial (only 3 species supported) | No | Yes | Yes | Yes | Yes |
| - Implementation | Intermine101 | No | Custom-designed solution | Intermine | Intermine | Custom-designed solution |
| Large-scale mutagenesis population & data | No | No | No | No | No | Yes; 121,531 LORE1 lines containing 629631 unique insertions |
| - Predicted gene model overlay | No | No | No | No | No | Yes |
| - Ordering and dispatching | No | No | No | No | No | Yes |
| BLAST | Yes; NCBI BLAST39 | Yes; NCBI BLAST | Yes; NCBI BLAST | Yes; NCBI BLAST | Yes; NCBI BLAST | Yes; SequenceServer38 powered by NCBI BLAST |
| - Programs | ||||||
| - - blastn | Yes | Yes | Yes | Yes | Yes | Yes |
| - - blastx | Yes | No | Yes | Yes | Yes | Yes |
| - - tblastn | Yes | No | Yes | Yes | Yes | Yes |
| - - tblastx | No | No | Yes | Yes | Yes | Yes |
| - - blastp | Yes | No | Yes | Yes | Yes | Yes |
| - Datasets | ||||||
| - - Genome | Yes | No | Yes | Yes | Yes | Yes |
| - - cDNA/mRNA | No | No | Yes | Yes | Yes | Yes |
| - - CDS | Yes | No | Yes | Yes | Yes | Yes |
| - - Proteins | No | No | Yes | Yes | Yes | Yes |
| - - Misc | – | Microarray chip target, sequences, and probes | – | Unspliced transcripts and BAC ends | – | LjGEA microarray chip probes |
| Gene expression | No | Yes | No | No | Yes | Yes |
| - Data transformation | No | Yes; normalization | No | No | Yes; normalization | Yes; normalization or standardization |
| - Data export | No | Yes; values are available as replica readouts or arithmetic means | No | No | Yes; only single values available in CSV format | Yes; values are available as replica readouts, arithmetic means, and pre-computed standard deviations |
| - Visualization | No | Yes; reliance on Adobe Flash, requires multiple windows to be opened | No | No | Yes; rudimentary and tabular based | Yes; using web-based data-driven approach, highly customizable |
| - Analysis | No | No | No | No | Yes; hierarchical clustering | Yes; asynchronous clustering—k-means or hierarchical—dependent on matrix size |
| - Co-expression analysis | No | Yes; single dimensional co-expression relationships | No | No | No | Yes; single and two-dimensional co-expression relationships, spatial network construction, and data-driven presentation |
| Public API | No | No | No | No | No | Yes |
| User documentation & help | Yes | Yes | No | Yes | Yes | Yes |
Abbreviations: BLAST, basic local alignment search tool; CDS, coding sequence; GEA: gene expression atlas.