At today, the BIOINforMA group can support you in the following analyses:

Genomics:

  • Reads quality check and cleaning
  • Genome masking
  • Preliminar genome gene structure annotation
  • Preliminar genome repeats annotation
  • Gene annotation structure quality check (via GFF)
  • GFF/GTF/BED files parsing and manipulation
  • Genome sequence extraction
  • Reads mapping
  • BAM/SAM file parsing and manipulation
  • Gene-mRNA-protein sequences extraction from GFF
  • Genome Composition (GC/CpG etc content)
  • Functional annotation (via BLAST vs UniProtKB/Swiss-Prot)
  • Functional annotation (via BLAST vs nr/nt)
  • Conserved Non-coding Elements (CNE) prediction
  • Orthology/Paralogy prediction
  • Complete comparative analysis via Comparo (orthologs-paralogs-networks)
  • Prokaryotic genome quality assessment (contamination vs. completeness)
  • Prokaryotic genome annotation (via Prokka)
  • Prokaryotic genome annotation (via Prokka on UniProt 90)

Transcriptomics:

  • Reads quality check and cleaning
  • Assembly & clustering
  • Reads/ESTs mapping
  • Reads count and RPKM calculation
  • DEGs calling
  • BAM/SAM file parsing and manipulation
  • Protein sequences prediction (via TransDecoder)
  • Functional annotation (via BLAST vs UniProtKB/Swiss-Prot)
  • Functional annotation (via BLAST vs nr/nt)
  • Functional annotation (via InterProScan, scanning 16 different databases, including protein domain, protein families and pathways databases)
  • Orthology/Paralogy prediction
  • Complete comparative analysis via Comparo (orthologs-paralogs-networks)

Metagenomics:

  • Assembly & clustering
  • Amplicon analysis (e.g. QIIME2)
  • Prokaryotic genome binning
  • OTU/ASVs/sOTUs table analysis and statistical analysis of microbiome studies
  • Multivariate analyses in microbial ecology
  • Evolutionary analyses (nucleotide and amino-acid phylogeny, phylogenetic networks, selection….)
  • Design and implementation of DNA barcoding projects

Protein analysis:

  • Functional annotation (via BLAST vs UniProtKB/Swiss-Prot)
  • Functional annotation (via BLAST vs nr)
  • Functional annotation (via InterProScan, scanning 16 different databases, including protein domain, protein families and pathways databases)
  • Orthology/Paralogy prediction
  • Complete comparative analysis via Comparo (orthologs-paralogs-networks)
  • Three-dimensional protein structure prediction (via homology modeling)
  • Molecular dynamics simulations

Additional services:

  • “Ad-hoc” file parsing

For any support, contact us!!!