Additional file 2: of BEACON: automated tool for Bacterial GEnome Annotation ComparisON

Contains the source code of BEACON in C++ for command line use along with makefile, a ReadMe file and the license text. (TGZ 42 kb

Additional file 3: Table S3. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

False positive and false negative rates comparison between DPS, DNN, and Omni-polyA derived by using different feature sets. (PDF 105 kb

Additional file 4: Figure S1. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

Nucleotide distribution for PAS variants in the PAS-weak category. These plots show the frequency of nucleotides for true PAS sequences in the 10 variants from the PAS-weak category. (PDF 1696 kb

Additional file 1: Table S1. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

Omni-PolyA feature set. List of the 218 numerical features. (PDF 104 kb

Additional file 7: Table S4. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

DPS, HMM_SVM and DNN model parameters. Parameters were determined from the validation set. (PDF 87 kb

Additional file 6: Figure S3. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

DNA structural profiles of the PAS-weak variants. Each structural profile is the average over all sequences from the PAS-weak variants (10 PAS variants). These plots show the actual average values (y axis) over all sequences for each position (x axis). (PDF 2412 kb

Additional file 8: Table S5. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

Omni-PolyA model parameters. Genetic algorithm parameters and feature set configuration determined from the validation set. (PDF 89 kb

Additional file 5: Figure S2. of Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

DNA structural profiles of the PAS-strong variants. These plots represent the 16 considered structural profiles. Each structural profile is the average over all sequences from the PAS-strong variants (AATAAA and ATTAAA). These plots show the actual average values (y axis) over all sequences for each position (x axis). (PDF 2541 kb

A) Gene Ontology, B) Protein Domain and C) Pathway enrichment analysis.

<p>The figure shows a snapshot obtained in case when a term “cell cycle” was searched through the keyword search option and resulting genes were saved in a list that shows enrichment of GO, protein domain and pathways in comparison to the rest of the data in INDIGO. The number of hits shown for reach category can be saved as lists for further analysis.</p

Region search interface.

<p>This figure shows features (genes) for a region using coordinates (Contig3:198625-229704) from organism <i>Haloplasma </i><i>contractile</i> (HLPCO). This region shows the cell Division and Cell Wall (DCW) biosynthesis gene cluster. An integrated genome browser view available via Region search results page, shows here the arrangement of genes in this region of the contig from HLPCO . The table below this section shows genome region, data export options, basic details of the feature (genes), type of features and their location on the genome. The create list by feature link saves this gene list in the data warehouse for further analysis. This list stays permanently if the user is logged in. </p