This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

Domenico Catalano*, Domenico Pignone, Gabriella Sonnante and Mariella M Finetti-Sialer*

Author Affiliations

Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Bari, 70126, Italy

For all author emails, please log on.

BMC Bioinformatics 2012, 13(Suppl 4):S12  doi:10.1186/1471-2105-13-S4-S12

Published: 28 March 2012

Additional files

Additional file 1:

predicted pre-miRNAs folding in Compositae. The table contain the information about all pre-miRNAs present in Carthamus tinctorius and Cynara cardunculus EST datasets. The table lists Embl/Genbank accession numbers, the fold image of the Cynara/Carthamus precursor and the orthologous extracted from miRBase database. In the last two columns we have reported the sub-sequence necessary to obtain the secondary structures.

Format: XLS Size: 901KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

RNAhybrid results in Carthamus tinctorius ESTs. The table lists the results of target prediction analysis carried out by RNAhybrid within the ESTs of Carthamus tinctorius. The parameter used in the analysis were: maximum one loop, one mismatch, and overhangs not longer than 2 nucleotides and mfe cut off value > 70% of the perfect match obtained by RNAHybrid.

Format: XLS Size: 2.6MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

RNAhybrid results in Cynara cardunculus ESTs. The table displays the RNAhybrid analyses of the target prediction within the ESTs of Cynara cardunculus. The parameter used in the analysis were maximum one loop, one mismatch, and overhangs not longer than 2 nucleotides and mfe cut off value > 70% of the perfect match obtained by RNAHybrid.

Format: XLS Size: 2.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Minimum free energy calculation for each miRNA target, by RNAhybrid. In the first and the second columns are reported the mirBase identifier and accessions numbers. In these two columns, the miRBase ID/accession have been listed by comma, for the species with identical mature miRNA sequence. For each mature miRNA the mfe and mfecut-off, used in the analysis, is indicated.

Format: XLS Size: 234KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Identified COS regions in Carthamus tinctorius and Cynara cardunculus. The table displays the COS regions shared by Carthamus tinctorius and Cynara cardunculus. Only the alignment of 400 bp or longer present in both species was considered. The position and the length of the fragment shared are recorded within each EST, as well as the values obtained in the BLAST analysis.

Format: XLS Size: 8.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Significant identified miRNA targets. The table contains the significant targets (specificity > 0.8) identified by this pipeline. For each target has been indicated the occurrence find in the ESTs, the average of the occurrence obtained considering two shuffled sequence datasets, the signal to noise ratio and the specificity.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Significant target functions. In the table are showed the statistical significant targets and the putative function obtained by comparison of the Cynara ESTs (representing one COS) against the Arabidopsis proteome.

Format: XLS Size: 263KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Arabidopsis Test 1. The table depicts 221 EST sequences as real pre-miRNA retrieved after BLAST analyses in Arabidopsis EST dataset. The analyses were conducted considering identity > 90%, and pre-micro sequence alignment coverage ≥ 70%, in order to limit the false positive originated from the possible targets.

Format: XLS Size: 59KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Arabidopsis Test 2. In the table are listed the pre-miRNA obtained on the same Arabidopsis EST dataset used for the real pre-miRNA identification (see Table S8), by the bioinformatic approach described in the manuscript. We recognised 196 out of 221, corresponding to 88% of the real precursor present in the data.

Format: XLS Size: 55KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data