Interpretation of DNA Sequence Data

1.     Read Sequence into computer

2.     Compare sequence with those in Genebank i.e. Blast and Fasta searches

3.     Download a number of similar sequences of known genotypes from Genebank or other libraries

4.     Compare visually and align if necessary

5.     Construct a phylogenetic tree using a phylogenetic analysis program.

Read Sequence

I used a program custom written by Dr. Peter Simmonds known as Simmonics

Compare Sequence with Genebank

1.     BLAST searches appear to be better than FASTA searches. However sequences deposited in Genebank have several problems.

2.     The actual genotypes of most of the viral sequences deposited in Genebank are not known

3.     Sequences deposited in Genebank are not refereed. e.g. one can make up a sequence and deposit it in Genebank as hepatitis Q

4.     A lot of the sequences deposited in Genebank are contaminated with plasmid vector seqeunces. This applies particularly to newly discovered viruses such as TTV.

Download a number of similar sequences

1.     This may actually be quite dangerous considering the problems with GENEBANK. It may be better to use complete genomes.

2.     However other libraries are available e.g. the Los Alamos set on HIV subtypes, other libraries may kept by individual researchers but are available through the internet.

Compare visually and align if necessary

1.     Again I import these sequences in Simmonics and make a visual check.

2.     The sequences should be aligned. If they do not align easily, look for insertions and deletions.

Construct a phylogenetic tree using phylogenetic program

·        This is by far the most difficult bit. A number of programmes are available for phylogenetic analysis, each with its advantages and disadvantages.

·        In Edinburgh, MEGA is generally preferred except for complete genomes when PHYLLIP is used.

·        A large number of options are available when carrying phylogenetic analysis.