Services
Please contact us if you desire assistance with any specialist bioinformatics problems.
Sequence Assembly
The end product of high throughput sequencing is a very large short DNA sequences, typically more than 10 million reads. Assembly is the process of producing a set of large contig sequences from these many overlapping reads. Our assembly service includes:
- Quality filtering and/or clipping of reads
- De novo sequence assembly using Velvet software from EBI
- Optimization of assembly parameters: k, coverage cut-offs, and insert length estimation
- Scaffolding of contigs (for paired-end reads)
- Tiling of contigs to a reference sequence and construction of a pseudo-molecule
Sequence Annotation
Annotation is the process of identifying all the relevant genomic features in contigs, most importantly genes. Our sequence annotation service includes:
- Identification of putative genes using a model trained on your own data
- Assignment of protein function to genes via homology searches
- Identification of putative signal peptide sequences
- Identification of tRNA and rRNA features
- Labelling of tandem repeat and inverted repeat regions
- Identification of putative operons
SNP Analysis
A single nucleotide polymorphism, or SNP, is a nucleotide difference between two otherwise identical DNA sequences. It could be a substitution, a deletion, or an insertion of a nucleotide.
- Identification of all SNPs between a reference genome and your reads
- Alternatively, SNPs between two or more sets of reads - no reference or assembly required
- A description of each SNP: truncated gene, frame-shift, amino acid change, intergenic region.
- A statistical significance for each SNP
Custom Services
Our team has skills and experience across a range of bioinformatic areas, garnered from years of collaboration with local and international researchers. For example:
- DNA microarray analysis
- Comparative genomics
- Discovery of DNA or protein motifs
- Identification of orthologous protein groups across multiple genomes
- Custom software development