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Bioinformatics Analysis Service

Sequence analysis

DNA :
Gene : promoters, coding regions, splice sites, effector binding sites, motif identification

Genome: High throughput alignments genome-on-genome, gene-wise, protein-wise, contig-vs-contig, multiple contigs against one, genome synteny, vector stripping

RNA : secondary structure prediction

Protein : small molecule binding sites, high throughput alignments protein-protein comparisons, motif identification, mapping proteins to COGs and GOs

Metabolites : pathways involved, binding to macromolecules, predicting metabolic routes from substrates to products

Expression analysis

Transcriptome (Microarrays only)

Platforms : Affymetrix, Nimblegen, Two-color arrays
Data normalization : RMA, GC-RMA, PLIERS, MAS 5.0, loess
Significance statistics : ANOVA for large scale data, pairwise comparisons, multiple comparisons, repeated measures
Data interpretation and visualization : GO Hierarchy analysis, heat maps by functional groups

Proteome (Protein expression profiles only)
Platform : LC-MS
Data normalization : By spike intensity
Significance statistics : ANOVA for large scale data, pairwise comparisons, multiple comparisons, repeated measures
Data interpretation and visualization : GO Hierarchy analysis, heat maps by functional groups

Metabolome (Metabolite profiles only)
Platform: LC-MS
Data normalization : By spike intensity
Significance statistics : ANOVA for large scale data, pairwise comparisons, multiple comparisons, repeated measures