Benefiting from molecular cloning and PCR techniques, DNA barcoding has now become a popular means for identification and authentication of plant and animal species. DNA barcoding is less affected by age, physiological condition of samples and environmental factors. The power of discrimination is so high that very closely related varieties can often be differentiated. The experiemental procedures can be divided into four steps: (1) Extraction of DNA from different samples; (2) amplification of DNA; (3) generation of species specific fingerprints or sequences and (4) sequence alignment and comparison.
Our primarily goal is to include the DNA barcodes recommended by CBOL. We also collect common supplementary barcodes as many studies point out that other regions are also useful in identification. As a result, MMDBD includes the following DNA barcodes:
(A) Nuclear genome
(B) Mitochondrial genome
(C) Chloroplast genome
Search: You can use any keyword less than 100 characters to search, which can be part of the species name, material name, family name, medical part or keyword in the title, journal or abstract of the reference. After obtaining the results, there is a species list at the bottom left. You may click one of the entries to get the sequence information at the right side of the list. When sequence information is clicked, a detailed layer will show all information about the sequence entry, including material information, sequence information and reference information if available. You can click “Import into BLAST for similar sequences” to submit the sequence to BLAST search, or click “Place into sequence cart” to put the sequence into sequence cart in FASTA format.
BLAST: Input a raw sequence data into the sequence text box. After obtaining the results shown, you may click the bar of alignment to get the overall information. Expect (E) value is an important parameter in BLAST search, which is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. The E-value of a BLAST search for the score S is determined by the number of letters in the database (n), the length of the query sequence (n), the values of K and Lambda (λ) based on the formula E=Kmne-λS. K and Lambda (λ) are the parameters in Karlin-Altschul statistics. Essentially, the E value describes the random background noise. It decreases exponentially as the Score (S) of the match increases. The lower the E-value, or the closer it is to zero, the more "significant" the match is.
Sequence cart: Sequences can be selected from Search or BLAST results and placed into sequence cart, where you can carry out different sequence manipulation, including complement, reverse or reverse complement.
Alignment and Primer Design: You can click “Use all the sequences in cart” to easily place the sequences into the field for multiple sequence alignment by Clustal Omega. The first sequence in the sequence cart will automatically be set as the source sequence, only from which short DNA segment can be selected. By highlighting the potential primer region and clicking “Select or Left/Right Primer”, the source sequence, and the two selected primer regions can be subjected to Primer3 for primer design.
Update:Currently we just provide a template file and support manual updating.