At today, the BIOINforMA group can support/collaborate with 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!!!Â