Question

Write a detailed guideline on how to analyze a random DNA sequence in FASTA format.

Answer 1

FASTA format is basically based on text used in the field of bioinformatics and biotechnology, it represents the amino acid sequence and by single letter code.

Here the DNA Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes:

• in amino acid sequences, the acceptable letters are U and * .
• lower-case letters are accepted and are mapped into upper-case;
• a single hyphen or dash can be used to represent a gap of indeterminate length;
• any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes.

DNA sequencing is the determination of neucleotides in the order of the four bases Adenine (A), Guanine (G), Cytosine (C) and Thymine (T), in a strand of DNA.

• DNA sequencing is carried out by using 4 vials in the following 4 steps:

Step 1: Denaturation

Step 2: Attachment of primers and extension of bases

Step 3: Termination

Step 4: Polyacrylamide gel Electrophoresis

According to FASTA format: ^[1]

The nucleic acid codes are:

        A --> adenosine           M --> A C (amino)
        C --> cytidine            S --> G C (strong)
        G --> guanine             W --> A T (weak)
        T --> thymidine           B --> G T C
        U --> uridine             D --> G A T
        R --> G A (purine)        H --> A C T
        Y --> T C (pyrimidine)    V --> G C A
        K --> G T (keto)          N --> A G C T (any)
                                  -  gap of indeterminate length

The accepted amino acid codes are:

    A ALA alanine                         P PRO proline
    B ASX aspartate or asparagine         Q GLN glutamine
    C CYS cystine                         R ARG arginine
    D ASP aspartate                       S SER serine
    E GLU glutamate                       T THR threonine
    F PHE phenylalanine                   U     selenocysteine
    G GLY glycine                         V VAL valine
    H HIS histidine                       W TRP tryptophan
    I ILE isoleucine                      Y TYR tyrosine
    K LYS lysine                          Z GLX glutamate or glutamine
    L LEU leucine                         X     any
    M MET methionine                      *     translation stop
    N ASN asparagine                      -     gap of indeterminate length 

( ^[1]Reference: The Yang Zhang Lab-University of Michigan )