The full abbreviation of DNA is the deoxyribonucleic acid.

The DNA ribbons are long polymers made of millions of nucleotides connected some to the others. Individually, nucleotides are simple chains consisting of three distinct parts. This includes one of the four nitrogenized bases, a deoxyribose (a sugar of 5 carbons), and a phosphate group. Whereas, A DNA sequence is composed by four nucleotides called as adenine, guanine, cytosine, and thymine, represented by the capital letters A, G, C, and T respectively. Adenine, and thymine are connected to each other to form a pair of AT bases, while guanine and cytosine form a pair of GC bases. The bases remain joined for weakly hydrogen bridges and these hydrogen bridges are responsible in order to maintain the structure of a double helix of the DNA sequence.

In late 1970's, two DNA sequencing techniques for longer DNA molecules were invented. These were the Sanger (or dideoxy) method and the Maxam-Gilbert (chemical cleavage) method. The Maxam-Gilbert method is based on nucleotide-specfic cleavage by chemicals and is best used to sequence oligonucleotides (short nucleotide polymers, usually smaller than 50 base-pairs in length). The Sanger method is more commonly used because it has been proven technically easier to apply and with the advent of PCR and automation of the technique is easily applied to long strands of DNA including some entire genes. This technique is based on chain termination by dideoxy nucleotides during PCR elongation reactions. In the Sanger method, the DNA strand to be analyzed is used as a template and DNA polymerase is used, in a PCR reaction to generate complimentary strands using primers. Four different PCR reaction mixtures are prepared each containing a certain percentage of dideoxynucleoside triphosphate (ddNTP) analogs to one of the four nucleotides (ATP, CTP, GTP or TTP). Synthesis of the new DNA strand continues until one of these analogs is incorporated, at which time the strand is prematurely truncated. Each PCR reaction will end up containing a mixture of different lengths of DNA strands all ending with the nucleotide that was dideoxy labeled for that reaction. Gel electrophoresis is then used to separate the strands of the four reactions in four separate lanes and determine the sequence of the original template based on what lengths of strands end with what nucleotide. In the automated Sanger reaction, primers are used that are labeled with four different coloured fluorescent tags. PCR reactions, in the presence of the different dideoxy nucleotides, are performed as described above. However, next, the four reaction mixtures

are then combined and applied to a single lane of a gel. The colour of each fragment is detected using a laser beam and the information is collected by a computer which generates chromatograms showing peaks for each colour, from which the template DNA sequence can be determined. Basic Local Alignment Search Tool (BLAST) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences and identify library sequences that resemble the query sequence above a certain threshold. This is the most frequently used tool for calculating sequence similarity. The BLAST algorithm and the computer program that implements it were developed by Stephen Altschul, Warren Gish, David Lipman at the U.S. National Center for Biotechnology Information (NCBI), Webb Miller at the Pennsylvania State University, and Gene Myers at the University of Arizona The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA. During the past five years many genomes have become searchable and the sequences in those databases are typically long chromosomes. Besides many long nucleotide sequences have been added to the BLAST databases as a result of highthroughput genomic projects. Previosly, sequences in the BLAST database have been associated with only one descriptive phrase that is normally the same as the definition in the GenBank flat file. This means that only very generic information is provided for matches to long database sequences even though such a sequence might have annotations for many genes, coding regions (CDS) and other features. Now we BLAST its very convinient for researchers in Bioinformatic and Biotechnology fields.