Bioinformatics is the application of statistics and computer science to the field of molecular biology and genetics. Its primary use has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing. The handling of data from high-throughput sequencing or huge-genome sequencing project requires a thorough expertise in statistics, bioinformatics and information technology. SolGent bioinformatics analysis team can offer customers this expertise in a standardized manner for expression profiling experiments. This insures that our customers receive fast and reliable results upon completion of genome analyses. Furthermore, these processes can be optimized to meet your individual project needs. Our bioinformatics service is continuously extended and validated. Analyzed data can comprehensively be annotated with information from various data sources, e.g. NCBI, Unigene, Enterez Gene, UniProt etc. Data can be provided in different formats as excel or as image file using own developed program.
1. Blast search
- BLASTP : compares protein sequence against protein database
- BLASTN : compares a nucleotide sequence against a nucleotide sequence database
- BLASTX : compares six-frame conceptual translation products of a nucleotide sequence against a protein sequence database
- TBLASTN : compares a protein sequence against a nucleotide sequence database translated in all reading frames
2. Whole genome sequencing(prokaryote)
Draft sequencing: Draft DNA sequence means a sequence of a DNA with less accuracy than a finished sequence. In a draft sequence, some segments are missing or are in the wrong order or are oriented incorrectly. Draft sequencing is a rapid and efficient method for determining the near-complete sequence of microbial genomes. Primary assembly data will be sent after GS FLX sequencing with gDNA library. Customer go to next step if the condition such as reference sequence, whole genome size and GC contents are available for gap filling
- De novo assembly (chromosome, ~11Mbp) :
De novo assembly is an assembly of sequencing reads without using supportive information derived from a related reference genome.
- Reference mapping :
GS-FLX produced read are connected together, and producing a couple of contigs and scaffold with a reference database. This process is called reference mapping.
- Gap filling :
each of contig and scaffold after draft sequencing and reference mapping is connected by filling their gap. This process is called gap filling.
- Chloroplast sequencing :
we provide chloroplast full sequencing service in plant. After sequencing and assembly(mapping), gap filling and annotation process are performed.
3. Genome Annotation
Gene annotation service refer to the vicarious execution service to predict OFR in DNA sequences and predict as well as gene characteristics through various homology and function searches.
- ORF find : ORF detection from complete sequence
- GO : Prediction OFR function comparison with GO data base by BLASTX
- COG : Making a graph to visualize based on GO result by category.
- Structural RNA : analysis of composition and dispersion of rRNA cassette and tRNA
- GC contents, GC skew : Analysis of GC ratio and nucleotide dispersion
4. Transcriptome analysis
Transcriptome analysis is using how altered expression of genetic variants contributes to complex disease such as cancer, diabetes, and heart disease. After cDNA library is conctructed, it is amplified and sequenced by GS-FLX sequencing. cDNA fragments are assembled and BLASTX are performed to analysis GO and COG.
5. Microsatellite (SSR)
Microsatellite, also known as short simple repeats(SSRs), are polymorphic DNA loci that contain a repeat sequence of 2-7 nucleotides. Data for allelic variation, the number of repeats, and allelic frequencies are available for thousands of markers across numerous organisms. SolGent detect microsatellite using RePick™, our innovative program, and repeat marker program with GS FLX sequenced read. Discovered microsatellites are confirmed by PCR & sequencing and performed genotyping with fluorescent tagging dye.
6. SNP ( Single Nucleotide Polymorphism )
Single Nucleotide Polymorphism (SNP) discovery studies provide valuable allelic variation information that can be used in genotyping experiments. The data generated by these studies is an important source of information for researchers across the globe. While the majority of SNP discovery studies focus on human genetics, we can apply the available technologies to allow experiments to be designed for any species of interest. We offer a comprehensive range of genotyping services from our purpose-built facility.
