Computational Systems Biology Methods and Protocols.7z

alignments are often preferable but can be more difficult to

calculate because of the additional challenge of identifying the

regions of similarity.

3.2 Methods and
Tools

There are various widely used DNA sequencing data analysis tools;

some are more familiar to us while some may not.

3.2.1 Two Types of DNA
Sequence Alignment

DNA sequence alignment can be divided into different types:

1. Pairwise alignment: it can only compare two sequences.


2. Multiple sequence alignment: it is an extension of pairwise
   alignment to incorporate more than two sequences at a time.

Several software are chosen to be discussed as follows.

3.2.2 BLAST BLAST, also known as Basic Local Alignment Search Tool (site:
blast.ncbi.nlm.nih.gov/Blast.cgi), is an algorithm to compare pri-
mary biological sequence information. Usually, you don’t have to
download and install it. All you have to do is to visit the website
stated above.
BLAST is actually a family of programs that is widely used in
bioinformatics; it enables us to make comparison between the
query sequence and a database of sequences. Those sequences can
belong to DNA, RNA, or protein. By selecting particular BLAST
tool and determining a certain threshold, we can identify sequences
that resemble the input sequence. For nucleic acid, there is
nucleotide-nucleotide BLAST (blastn). After putting in a DNA
query and setting certain parameters, we get results showing the
most similar DNA sequences.
Blastn does its job by locating short matches. Usually, there is a
threshold scoreT. If the score is higher than a predeterminedT, the
alignment will be included in the results given by BLAST and vice
versa. Therefore, choosing a proper value ofTmeans getting a
proper amount of results.
This tool is highly sensitive and can be utilized for several
purposes: species identification, domains location, phylogeny
establishment, etc.

1. Visit the site blast.ncbi.nlm.nih.gov/Blast.cgi and choose
   blastn.


2. Upload your DNA sequence in proper format like FASTA.


3. Set proper parameters includingT.


4. Click BLAST.


5. Reviewing your alignment results; mismatches can be a frame-
   shift in the query sequence.


6. If any error exists, go back, check the sequence file, change
   values of parameters, and BLAST again.

10 Keyi Long et al.