Tools
Blast Server
We have a public blast server that provides access to some of the datasets generated by members of the group. There you can find our current polyploid genome assembly for SP80-3280 (assembly B2) and a version of a pan-transcriptome assembly (longest transcript of group, Scp.v1) derived from 50 sugarcane genotypes.
The following databases are available in our blast server:
| DB name | DB type | Description | Number of sequences in DB |
|---|---|---|---|
| B2.p_utg.GENOME | Nucleotide | ShowDraft genome sequence of cultivar SP80-3280 version B2 | 128247 |
| B2.p_utg_BRAKER3.CDS | Nucleotide | ShowBRAKER annotation of genome sequence of cultivar SP80-3280 version B2 - Coding sequences | 257198 |
| B2.p_utg_GALBA.CDS | Nucleotide | ShowGALBA annotation of genome sequence of cultivar SP80-3280 version B2 - Coding sequences | 722191 |
| sugarcanePanTranscriptome_CDS | Nucleotide | ShowSugarcane pantranscriptome from 50 cultivars - Coding sequences | 9635835 |
| sugarcanePanTranscriptome_CDS_representatives | Nucleotide | ShowSugarcane pantranscriptome from 50 cultivars - Longest coding sequence per similarity group | 600931 |
| sugarcanePanTranscriptome_transcript | Nucleotide | ShowSugarcane pantranscriptome from 50 cultivars - Transcript sequences, may contain UTRs | 16931413 |
| sugarcanePanTranscriptome_transcript_representatives | Nucleotide | ShowSugarcane pantranscriptome from 50 cultivars - Transcript sequence for the transcript with the longest CDS, may contain UTRs | 600931 |
| B2.p_utg_BRAKER3.PEP | Protein | ShowBRAKER annotation of genome sequence of cultivar SP80-3280 version B2 - Protein sequences | 257198 |
| B2.p_utg_GALBA.PEP | Protein | ShowGALBA annotation of genome sequence of cultivar SP80-3280 version B2 - Protein sequences | 722191 |
| sugarcanePanTranscriptome_protein | Protein | ShowSugarcane pantranscriptome from 50 cultivars - Protein sequences | 5742563 |
| sugarcanePanTranscriptome_protein_representatives | Protein | ShowSugarcane pantranscriptome from 50 cultivars - Protein sequence for the transcript with the longest CDS | 600931 |
Further details about the sugarcane pan-transcriptome can be found in the Felipe Vaz Perez Master Dissertation.
Further details about the sugarcane genome of cultivar SP80-3280 version B2, can be found in this presentation.
Digital Northern
We took the 20 year-old data generated as part of the SUCEST project, and made a new minning application of gene expression values per library, available here, the EST libraries shown there are described in this paper. We created this app, because this dataset is the only one available that includes callus.
We also created a new app, with expression values of genes annoted in our new genome assembly of cultivar SP80-3280. This will be available for the time being until we have the final version of the assembly and annotation adn move everything into Conekt Grasses.
CoCoView
Are you interested in visualizing codon conservation from multiple sequences alignments. The traditional implementation of SequenceLogos cannot do that, this is why we developed CoCoView, check our tool and its companion paper.
PloidyNGS
You have a reference genome, some short read genomics data, and whant to get a feeling of the ploidy of you object of study, say no more, use our tool PloidyNGS, check out also its companion paper