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The Need For Collecting and Storing The Sequence of DNA Molecules in Computer Files

DNA sequencing involves determining the order of nucleotides in a DNA molecule. It is done by collecting and storing DNA sequences in computer files. Computers are crucial for DNA sequencing as they automate the sequencing process, greatly reduce the time required, and help assemble sequenced reads back into the original DNA sequence. While powerful computers are needed for genome assembly, DNA sequencing still faces limitations such as errors and high costs. New techniques like nanopore sequencing that can sequence long DNA strands directly are helping to address these issues.

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Subodh Shriv
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55 views

The Need For Collecting and Storing The Sequence of DNA Molecules in Computer Files

DNA sequencing involves determining the order of nucleotides in a DNA molecule. It is done by collecting and storing DNA sequences in computer files. Computers are crucial for DNA sequencing as they automate the sequencing process, greatly reduce the time required, and help assemble sequenced reads back into the original DNA sequence. While powerful computers are needed for genome assembly, DNA sequencing still faces limitations such as errors and high costs. New techniques like nanopore sequencing that can sequence long DNA strands directly are helping to address these issues.

Uploaded by

Subodh Shriv
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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The need for collecting and

storing the sequence of DNA


molecules in computer files
Subodh Shrivastava
B.Tech ADE B4
SAP ID: 500052981
What is DNA sequencing ?
• DNA sequencing is the best method for collecting and storing the
sequences of DNA molecules in computer files.

• It’s a process of determining the precise order of the nucleotides within


a DNA molecule.

• The four nucleotides are namely —adenine, guanine, cytosine,


and thymine.

• A DNA sequencer is basically a computer used to automate the DNA


sequencing process.
One of the Sequencing techniques :
• The basic reaction mixture contains - the template DNA, free nucleotides, an
enzyme and a primer (a small piece of single stranded DNA) .

• The reaction is initiated by heating until the two strands of DNA separate, then
the primer sticks to its intended location and then starts to elongate.

• The process results in formation of a new strand of DNA .

• Therefore , If we start with a billion pieces of template DNA that are identical ,
we'll get a billion new copies of one of its strands.

• These bases on the strands can now be mapped back to their original locations.
Why do we use computers for DNA
sequencing ?
• DNA sequencing is an extremely intensive , repetitive and cumbersome
process.

• Without computers , the sequencing of whole genomes would be close to


impossible.

• Computers largely reduce the time required for the process to complete.

• The amount of errors have also been greatly reduced with the
improvement in the technology of the DNA sequencers.
What happens in the DNA sequencers ?
• In current sequencing platforms the DNA is split into many small
pieces and then analyzed.

• What we get is millions or even billions of short strings of A, C, G, and


T representing the nucleotides of a single fragment of DNA !

• The DNA reads in this form aren't particularly useful. This is where the
genome assembly software come in.

• These software find the optimal arrangement of overlapping reads ,


thereby determining the original sequence of the genomic DNA.
• Computers are needed at two stages of the process described in the
last slide-
1. In the sequencing experiment , fluorescent signals are recorded and
interpreted to generate the sequence reads through computers.

2. To assemble the reads back into a adjacent sequence to recover the


original DNA sequence (very powerful computers are needed for
accomplishing this task) .
Limitations in the DNA sequencer technology
• In sequencing the genome of the fruit fly, every bit of the capacity of
the a supercomputer was used . Now imagine the sequencing of a
human genome.
• The process is prone to errors – mainly due to errors in the
sequencing techniques or errors during amplification.
• The process is also quite costly.

• Therefore, we can say that having these machines in doctor’s clinics


would take some time.
A new approach- Nanopore sequencing
• Nanopore sequencing can handle long strands of DNA at once, thus
the need for overlap analysis is eliminated (which was previously
done by computers).

• Single DNA strands are threaded through extremely tiny pores in a


membrane.

• The bases are read one at a time.


Summary:

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