Different types of sequences - Bioinformatics

cDNA : A large number of sequences deposited in the Databases were determined from cDNA molecules. While filling up the sequence entry form you must tick at the right position to indicate whether the sequence being deposited is a cDNA sequence. This data will also be provided when a sequence is retrieved. Thus in the case of cDNA sequences one is looking at the expressed part of the genome.

Genomic DNA: Sequencing of genomic DNA has become very routine nowadays. The genomic DNA is the store-house of information of which expressed part is represented in the cDNA sequences also.

ESTs : It is an abbreviation for Expressed Sequence Tags. Dr. Craig Venter initiated sequencing of a large number of cDNA molecules by sequencing one end of each of the randomly picked cDNA clones. Millions of ESTs have been deposited in a special database called dbEST. EST data is used to infer expression patterns by counting the number of ESTs corresponding to each gene divided by the total number of ESTs.

GSTs : In Plasmodium falciparum the enzyme Mung Bean Nuclease (MNase) cleaves in between the genes. A genomic DNA library generated by digestion with MNase was used for gene identification in P. falciparum. The approach used was similar to ESTs. One read of sequence was obtained from either ends. This data is referred to as genome sequence tags (GSTs). Usually, genomic DNA sequence refers to the nuclear DNA.

Organelle DNA: Eukaryotic cells have organelles such as mitochondria and chloroplast. These organelles have their own store house of information in the form of organelle DNA. Organelle DNA codes for a few genes. The coding information for the rest of the genes reside in the nuclear DNA of the same cell. If an organelle DNA has been sequenced the appropriate position in the sequence submission form must be mentioned.

Other molecules: In addition to these molecules, the databases contain the sequences of other molecules such as tRNA, and other small RNAs.