Different
types of sequences
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.
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