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Additional file 4: File S3. of MicroRNA categorization using sequence motifs ...
PhyloXML formatted phylogenetic tree: This file can be directly uploaded to Itol or other phylogenetic tree viewers for further analysis. (TXT 7Â kb) -
Additional file 3: Table S3. of Cnidaria: fast, reference-free clustering of ...
Statistics of k-mer counting. Total number of k-mers in each sample, total number of valid k-mers in each sample (k-mers shared by at least two samples) and the percentage of... -
Additional file 6: Table S6. of Cnidaria: fast, reference-free clustering of ...
List of samples used for the 1-nearest-neighbour analysis for species classification and their respective taxonomic ranks. (XLS 26Â kb) -
regression analysis
Notes: standard errors in parentheses; * p< 0.10, ** p< 0.05, *** p< 0.01; Estimates have been performed with Stata 13. 1 χ -(1)2is an Lr test on the null... -
dedup_wf_001--ad32c54fa1ebf645ed460d99412d7cc9
Raw data for three separate urban forest samples of the city of Meran in Northern Italy. One is a random sample following I-tree protocol, one is a public tree inventory... -
Additional file 3: File S2. of MicroRNA categorization using sequence motifs ...
Newick formatted phylogenetic tree: This file can be directly uploaded to Itol or other phylogenetic tree viewers for further analysis. (TXT 2Â kb) -
dedup_wf_001--7cca8b41a7fd61746dd4b189713dd546
Sample description. Intermediate headers show database size and analysis time running with 1 thread (1×) or 20 threads (20×) for each CNIDARIA database group. Each line contains... -
Additional file 4: Table S4. of Cnidaria: fast, reference-free clustering of ...
Matrix containing pairwise Jaccard distance between samples. The diagonal is blanked but contains zeroes, meaning identity; 11, 15, 17, 21 and 31-mers are shown, as well as the... -
Limitations of alignment-free tools in total RNA-seq quantification
Background Alignment-free RNA quantification tools have significantly increased the speed of RNA-seq analysis. However, it is unclear whether these state-of-the-art RNA-seq... -
Assessment of k-mer spectrum applicability for metagenomic dissimilarity anal...
Background A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates... -
Cnidaria: fast, reference-free clustering of raw and assembled genome and tra...
Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying... -
MicroRNA categorization using sequence motifs and k-mers
Background: Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency.... -
The khmer project v2.1
The source code for version 2.0 of the khmer project. http://khmer.readthedocs.org/ -
Additional file 7: Table S7. of Cnidaria: fast, reference-free clustering of ...
1-nearest-neighbour accuracy results for all k-mer sizes, distance measures and programs. CNIDARIA is tested against all k-mer sizes. REFERENCEFREE is tested using 21-mers.... -
Additional file 5: Table S5. of Cnidaria: fast, reference-free clustering of ...
List of samples used for the 1-nearest-neighbour analysis for supra-species classification and their respective taxonomic ranks. (XLS 29Â kb)
