Basic Local Alignment Search Tool (BLAST)

By: Ingrid Lobo, Ph.D. (Write Science Right) © 2008 Nature Education
Citation: Lobo, I. (2008) Basic Local Alignment Search Tool (BLAST). Nature
Education 1(1)

Awash in a sea of data, how do scientists identify the function of a newly cloned
gene? Online resources like the Basic Local Alignment Search Tool (BLAST) provide a
helping hand.

Since the discovery of the genetic code, biological research has undergone a sea change in the way
it is performed. Until the early twentieth century, biology focused on the processes of living
organisms and almost always involved experiments in laboratories and in the field. The growth of
molecular biology in the twentieth century moved research into the test tube, where biological
systems could be painstakingly dissected and reassembled. Then, beginning in the 1970s,
scientists began to accumulate DNA and protein sequence data at an exponential rate; in fact,
researchers currently have approximately 97 billion bases sequenced and over 93 million records.
Amazingly, this sequence data doubles every 18 months!

But how do investigators search through, organize, and make sense of this massive amount of
data? And how can they identify the functions of newly cloned genes? Is it possible to estimate the
evolutionary relationships between genes or proteins just by examining their nucleotide or amino
acid sequences? The answer to this question is yes. The relationships between organisms can be
teased out as different species are connected via descent from a common ancestor. Thus,
sequence similarity can be helpful in inferring function and evolutionary relationships. One
common way to examine a new gene is to search for similarities between newly sequenced DNA
and databases of gene sequences that have already been described. By identifying a related gene
or gene family with a known function, scientists can infer the function and evolutionary
relationships of newly cloned genes or even whole genomes. If genes have similar sequence
regions, then the genes may share similar functions.

As gene and protein sequence databases grew at the end of the twentieth century, scientists
turned to computers to help analyze the abundant and ever‑growing amounts of data. Today, one
of the most commonly used tools to examine DNA and protein sequences is the Basic Local
Alignment Search Tool, also known as BLAST (Altschul et al., 1990). BLAST is a computer algorithm
that is available for use online at the National Center for Biotechnology Information (NCBI) website
and many other sites. BLAST can rapidly align and compare a query DNA sequence with a database
of sequences, making it a critical tool to ongoing genomic research. In fact, the initial paper
describing the program, titled "Basic Local Alignment Search Tool" and published in the Journal of
Molecular Biology, was the most highly cited publication of the 1990s (Taubs, 2000). The parallel
development of large‑scale sequence projects and bioinformatic tools like BLAST has enabled
scientists to study the genetic blueprint of life across many species and has helped bridge the gap
between biology and computer science in the maturing field of bioinformatics.

Alignment Theory
While the computer science principles behind BLAST have been around for some time, prior to
BLAST, they had not been applied to biology. Before BLAST, alignment programs used dynamic
programming algorithms, such as the Needleman‑Wunsch and Smith‑Waterman algorithms, that
required long processing times and the use of a supercomputer or parallel computer processors
(Collins & Coulson, 1984; Gotoh & Tagashira, 1986; Smith & Waterman, 1981).

Figure 1A depicts a Needleman‑Wunsch alignment of the words "PELICAN" and "COELACANTH."

The search space of the alignment is shown using a Cartesian grid and is proportional to the
length of the sequences being compared plus one extra row and column.

Figure 1A: Initialization of the alignment

matrix.
A Needleman‑Wunsch alignment of the
words "PELICAN" and "COELACANTH."
Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992

Next, the alignment matrix is initialized with a zero in the upper left corner. For each letter of the
word being aligned, a point is deducted so that each letter has a progressively more negative
score. Why does the algorithm subtract a point? In an alignment, the diagonal is read from the
upper left to the lower right, and when the analysis moves vertically or horizontally, it indicates a
gap in the sequence. Thus, each time the program moves straight up or down, a gap penalty is
applied that takes away points from the alignment score. Finally, a little arrow, or pointer, is added
to indicate which direction to follow the alignment (Figure 1B).
 Figure 1B: Filling the axes of the
alignment matrix.
When filling the axes of the alignment
matrix, start in the upper left corner and set
it to 0. Next, assign a score for each letter in
the row or column. Note that there is a
penalty for gaps, and that the arrow should
point toward the origin of the alignment.
Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992

In the third stage, the algorithm starts to actually build and score the alignment in a step called fill
or induction. In this example, the analysis begins by aligning the C to the P and calculating a
score. In Figure 1C, one point is added if two letters match, and one point is subtracted if they do
not. This calculation is carried out three times, once for each square to the left (dark blue), above
(green), and upper left (brown). Using a value from either the upper or left square, the final score
is ‑2 (‑1 + ‑1). Using the 0 score in the upper left diagonal square, the final score is ‑1 (0 + ‑1).
Because ‑1 is the highest score, this score is jotted down in the alignment matrix, and because the
upper left square was the one leading to the best score, an arrow is inserted in the box pointing
toward this square (light blue, Figure 1C).
 Figure 1C: Induction or filling of the
alignment matrix, part I.
One point is added if two letters match, and
one point is subtracted if they do not. Using
a value from either the upper (green) or left
(dark blue) square, the final score is ‑2;
however, using the value from the upper left
(brown) square, the final score is ‑1. Because
this is the highest score, it is recorded in the
alignment matrix along with an arrow
pointing to the upper left square.
Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992

This same process continues, calculating two scores for every square in the matrix (Figures 1D and
1E).
 Figure 1D: Induction or filling in of the
alignment matrix, part II.
The same process is carried out for the next
square in the alignment. Here, using the
value in upper left (brown) square yields a
sum of ‑2, using the value in the upper
(green) square yields a sum of ‑3, and using
the value in the left (dark blue) square yields
a sum of ‑2. Because ‑2 is the highest score
and was initially calculated using the upper
left square, ‑2 is recorded in the matrix
along with an arrow pointing toward the
brown square.
Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992
 Figure 1E: Induction or filling in of the
alignment matrix, part III.
The rest of the matrix is completed using the
same method.
Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992

Once the matrix is completed, the optimal alignment is found through a process called traceback.
The traceback starts in the lower right of the matrix and follows the pointers to adjacent boxes. By
definition, traceback involves determining the best scoring path through the alignment (Figure 1F).

Figure 1F: Traceback of the optimal

complete alignment.
During traceback, following the best scoring
path reveals the best alignment.
 Copyright 2003 O'Reilly Media Inc. All
rights reserved. Used with permission.
Korf, I., Yandell, M., & Bedell, J., BLAST.
ISBN: 9780596002992

Although this sort of dynamic programming did a complete job of comparing every single residue
of one sequence to every single residue of a second sequence and kept track of how well the
sequences aligned at every step, these algorithms required a considerable amount of computer
memory and processing time. Computing speed was an especially important concern, because
these exhaustive programs had to search databases that continued to grow at exponential rates.
Moreover, most regions of the search space did not score very well and therefore probably could
have been skipped during the calculation process. Finally, these programs required powerful
computing hardware that was expensive, rare, and ultimately impractical for most scientists and
labs.

Researcher Stephen Altschul and colleagues wanted to bypass these challenges and develop a way
for databases to be searched quickly on routinely used computers. In order to increase the speed
of alignment, the BLAST algorithm was designed to approximate the results of an alignment
algorithm created by Smith and Waterman (1981), but to do so without comparing every residue
against every other (Altschul et al., 1990). BLAST is therefore heuristic in nature, meaning it has
"smart shortcuts" that allow it to run more quickly (Madden, 2005). However, in this trade‑off for
increased speed, the accuracy of the algorithm is slightly decreased.

The BLAST Heuristic

BLAST increases the speed of alignment by

decreasing the search space or number of
comparisons it makes. Instead of comparing
every residue against every other, BLAST uses
short "word" (w) segments to create alignment
"seeds." BLAST is designed to create a word list
Figure 2: Generating word seeds.
from the query sequence with words of a specific
length, as defined by the user (Figure 2). Instead of comparing every residue against
Requiring three residues to match in order to each other, BLAST uses short “word” (w)
seed an alignment means that fewer sequence segments to create alignment "seeds." BLAST
regions need to be compared. Larger word sizes is designed to create a word list from the
usually mean that there are even fewer regions to query sequence with words of a specific
evaluate (Figure 3A versus Figure 3B). Once an length, as defined by the user.
alignment is seeded, BLAST extends the Copyright 2003 O'Reilly Media Inc. All
alignment according to a threshold (T) that is set rights reserved. Used with permission.
by the user. When performing a BLAST query, the Korf, I., Yandell, M., & Bedell, J., BLAST.
computer extends words with a neighborhood ISBN: 9780596002992
score greater than T (Figure 3C). A cutoff score
(S) is used to select alignments over the cutoff, which means the sequences share significant
homologies. If a hit is detected, then the algorithm checks whether w is contained within a longer
aligned segment pair that has a cutoff score greater than or equal to S (Altschul et al., 1990). When
an alignment score starts to decrease past a lower threshold score (X), the alignment is terminated
(Figure 3C). These and many other variables can be adjusted to either increase the speed of the
algorithm or emphasize its sensitivity.

Testing the BLAST Algorithm

Altschul and colleagues tested the BLAST algorithm on a database of
randomly generated sequences, and they examined the output resulting from
different w and T parameters. If T is set to be a lower threshold, then the
algorithm detects more word pairs and requires a longer processing time
(Altschul et al., 1990). Choosing the value for T was a major decision because
the researchers wanted to reach a compromise between the algorithm's
sensitivity and its processing time.

Next, Altschul and colleagues tested BLAST on a database of real sequences,

and they found it was successful in quickly identifying alignments with high
scores. In searching the globin gene family, for example, they found that
BLAST identified 88 of the 89 globin alignments that scored above 80. Other
gene families, including the immunoglobulins, protein kinases, and
cytochrome c genes, were then examined to measure the number of
Figure 3
alignments detected when using different T and S values. BLAST was also
able to detect similar regions within pairs of long sequences. These tests
showed that BLAST was fast, sensitive, and accurate as a tool for analyzing sequence alignments
(Altschul et al., 1990).

Bringing Mathematical Rigor to Alignment

One of the most notable innovations of BLAST is that the program calculates the statistical
significance for each sequence alignment result. This is known as the expect value (E‑value) or
probability value (P‑value), and it is calculated for each alignment. The E‑value describes how
many hits you can expect to see by chance when searching a database of a certain size, whereas
the P‑value describes the probability that the alignment you are observing is due to chance. In
general, the lower the E‑ or P‑value is, the more likely it is that an alignment is significant. Below
the common 10‑5 score, P and E are roughly equivalent (Madden, 2005).

The addition of statistical rigor to sequence alignment has been controversial. Some researchers
rely too much on significance values to include or exclude sequences despite poorly chosen
parameters, while others overinterpret "insignificant" results because the results "look" right. While
all scientific results are subject to interpretation, BLAST scores and statistics bring much‑needed
objectivity to sequence comparisons, and the debate about them has helped improve methods for
determining significance.

The BLAST Family

Since 1990, many variants of BLAST have been developed, each with specialized features. Early on,
the original BLAST was split into two adaptations: NCBI BLAST and Washington University BLAST
(WU BLAST). Both BLASTs have program variations. For instance, BLASTN can be used to compare a
nucleotide sequence with a nucleotide database; BLASTP can be used to compare a protein
sequence with a database of protein sequences; and BLASTX can take a nucleotide sequence,
translate it, and query it versus a protein database in one step (Gish & States, 1993). TBLASTN
compares a protein query sequence to all six possible reading frames of a database and is often
used to identify proteins in new, undescribed genomes. Finally, TBLASTX compares all six reading
frames of a query sequence to all six reading frames of a database—an intensive algorithmic feat
that can bring even modern computers to a grinding halt if not used properly.

In addition, NCBI has some of its own specialized variants of BLAST. For example, MEGABLAST is a
program that can rapidly complete searches for sequences with only minor variations and can
more efficiently manage queries with longer sequences (Altschul et al., 1994). PSI‑ and PHI‑ are
other powerful BLAST tools that allow more complex and evolutionary divergent proteins to be
aligned (Altschul et al., 1997). These and other programs, as well as genomic BLAST databases, are
all available on the NCBI BLAST website.

Since its creation, BLAST has become an essential bioinformatics tool for biologists. Its speed and
sensitivity allow scientists to compare both nucleotide and protein sequences to single sequences
and to large databases. Most importantly, BLAST has helped democratize bioinformatics analysis
and make it accessible to any researcher over the Internet. It is rare to read a modern molecular
biological paper that does not refer to a BLAST alignment, and this information has permitted
scientists to predict the functions of genes and proteins in whole genomes, answering questions in
silico that could never be answered at a bench or in the field.

References and Recommended Reading

Altschul, S. F., et al. Basic Local Alignment Search Tool. Journal of Molecular Biology 215, 403–410
(1990) doi:10.1016/S0022‑2836(05)80360‑2 (link to article)

Altschul, S. F., et al. Issues in searching molecular sequence databases. Nature Genetics 6, 119–129
(1994) doi:10.1038/ng0294‑119 (link to article)

Altschul, S. F., et al. Gapped Blast and PSI‑Blast: A new generation of protein database search
programs. Nucleic Acids Research 25, 3389–3402 (1997)

Collins, J. F., & Coulson, A. F. Applications of parallel processing algorithms for DNA sequence
analysis. Nucleic Acids Research 12, 181–192 (1984)

Gish, W., & States, D. J. Identification of protein coding regions by database similarity search.
Nature Genetics 3, 266–272 (1993) doi:10.1038/ng0393‑266 (link to article)

Gotoh, O., & Tagashira, Y. Sequence search on a supercomputer. Nucleic Acids Research 14, 57–64
(1986)

Korf, I., Yandell, M., & Bedell, J. BLAST: An Essential Guide to the Basic Local Alignment Search Tool
(O'Reilly, Sebastopol, CA, 2003)

Madden, T. The BLAST sequence analysis tool. In NCBI Handbook, ed. J. McEntyre and J. Ostell
(National Library of Medicine, Bethesda, MD, 2005)

Smith, T. F., & Waterman, M.S. Identification of common molecular subsequences. Journal of
Molecular Biology 147, 195–197 (1981) doi:10.1016/0022‑2836(81)90087‑5

Taubs, G. Sense from sequences: Stephen F. Altschul on bettering BLAST. Science Watch 11, 3–4
(2000)

Outline | Keywords | Add Content to Group