Objective 

To find  primers from a given nucleotide sequence

 Theory

DNA (Deoxyribonucleic acid) is the genetic material that contains the genetic information for the development and maintaining all functions in living organisms. The information is stored as genetic codes using four types of nucleotides. They are adenine (A), guanine (G), cytosine(C) and thymine (T). In two strands of DNA, adenine always pair with thymine and guanine pair with cytosine. Each of these base pairs will bond with a sugar and phosphate molecule to form a nucleotide. The base pairing of DNA will result in a ladder shape structure of these strands which is called a double helix. DNA replication is a mandatory biological process to maintain life where a single set of DNA gives rise to two copies of DNA. The process of DNA replication is catalyzed by an enzyme named DNA polymerase. These enzymes are able to add nucleotides only to an existing DNA strands.

A primer can be defined as short nucleic acid sequences. It can act as a starting point for DNA synthesis. The polymerase enzyme starts adding nucleotides in the 3’-end of the primer. Process like DNA sequencing (to determine the exact order of nucleotides in a DNA) and polymerase chain reaction (or PCR, used to amplify DNA sequences) require DNA primers whereas for natural DNA replication short sequences of RNA is used as primer. Usually the length of the primer is 18 to 24 nucleotides.

Since primer has a very important role in most of the experiments in biochemistry and molecular biology, it is essential to choose these sequences correctly.

ApE is a tool which can be used to find primers from a given sequence. Some of the features of ApE are given below:

1. Runs in Linux and Windows OS
2. Able to highlight the text using pre-defined custom feature libraries which allows for quick searching and highlighting of all the available primers, quick annotation of the sequence, searching sequences to be annotated etc.
3. Searches for possible primers that matches with the length, GC content, Tm etc. which user specifies.
4. Reads file formats such as FASTA, Genbank, EMBL and formats from DNA Strider.
5. Save files in Genbank format or DNA Strider-compatible format.
6. Allows direct BLAST search in NCBI.
7. Highlights restriction sites from the input.
8. Shows Tm (melting point), GC content of the sequence, ORF in a sequence.
9. Translate the input sequence by means of an optional DNA alignment.
10. Draw and highlight the graphical maps from Genbank and EMBL files through its feature annotations.

Figure 1 shows the GUI of ApE.

Figure 1: ApE GUI