The Difference is in the Data Analysis
The more of the sequence that is analyzed, the higher confidence we have in the answer. This is why we never produce an identification report using anything other than the entire sequence.
The analysis of DNA sequence data is a complex process. We use the same high accuracy reference method to interpret your data that we use to create our library entries. This is not the case with other commercial solutions. There are several steps which require an experienced scientist to make decisions about DNA sequence quality, DNA sequence assembly and phylogenetic relatedness in order to correctly analyze and interpret the data. Results of the highest quality and accuracy are obtained with our manual process of data analysis and interpretation.
Our Microbial Phylogeneticists first confirm the data are of a high enough quality to generate an identification report. The initial data quality check is performed using our propriety software to classify the data as acceptable, not acceptable or requires verification. Other commercially available automated sequencing systems will automatically reject or truncate some data for inappropriate reasons causing erroneous results. For example, data from an organism that contains multiple copies of the 16S rRNA gene may have an insertion/deletion (Indel event) in some of the copies, resulting in data that appears to be derived from a mixed culture. However, our experienced Microbial Phylogeneticists can easily decipher the difference between mixed and Indel sequences utilizing a proprietary software program to resolve the Indel events and also identify and interpret areas that contain polymorphisms.
After the sequence has been generated from the sample, the software from other commercially available systems will remove nucleotides from the ends of the sequence until an acceptable quality score is reached. Depending on the overall quality of the DNA sequence, the number of nucleotides removed during an automated process can range from 40 to 450 of the approximately 500 nucleotides in the sequence.
Our scientists will ensure that our analysis uses the entire sequence generated from the PCR product. We analyze the entire sequence from primer to primer. Our experience has proven that the most accurate distance measurements, and therefore the most accurate identifications, are generated using as much of the DNA sequence as possible.