Bacterial Common Gene Finding Using

Distributed Workload Management

NORRASETH CHANTASUT , NOPPADON KHIRIPET
High Performance Computing Research and Development Division,
National Electronics and Computer Technology Center,
112 Thailand Science Park,
Klong Luang, Pathumthani 12120
THAILAND
norraseth.chantasut@nectec.or.th, noppadon.khiripet@nectec.or.th

Abstract a supervised learning approach to predict yeast gene

Bioinformatics can be defined as the creation and
development of advanced information and
computational techniques for problems in biology. It
consists of computing techniques used to manage and
extract useful information from the DNA/RNA/protein
sequence data. In many cases, the methods for
analyzing genetic/protein data have been found to be
extremely computationally intensive, thus providing
motivation for the use of powerful computer systems
such as supercomputer, cluster computing, and grid
computing. We build upon the cluster computing
technology a distributed workload management to
partition problem the space and manage the
comparison tasks. Our preliminary results show that
the distributed workload management can be well
achieved in a bacterial common genes finding
application.
Key-Words: Bioinformatics, Genome Comparison,
Common Gene Finding
1. Introduction
Bio-data analysis is an important task in
Bioinformatics. It concerns with problem domains
such as gene finding, the determination of protein
function, the identification of co-occurring bio-
sequences, and gene pathway analysis. For example,
Vladimir Filkov, Steven Skiena and Jizu Zhi
proposed integrated analysis method of yeast gene
expression data [1]. Jack Y. Yang, Okan K. Ersoy
and Mary Qu Yang proposed a new two-stage
approach to determine of protein function and gene
finding that uses both unsupervised learning and
supervised learning techniques [4]. Lev A Soinov,
Maria A Krestyaninova, and Alvis Brazma proposed
expression data [5].
Recently, similarity search and gene sequences
comparison of bacterial genomic data become
important task in Bioinformatics [2],[3]. Because the
research may lead to the discovery of new drug
targets. The problem on similarity search and
comparison of bacterial genome data is often time-
consuming due to a large number of both bacterial
species and their genes. To reduce the processing
time, high performance computing systems can be
applied to the problem of comparing gene sequences
of bacterial genomic data.
The high performance computing system can
perform a specific task with much better performance
than ordinary computing system. The task can be of
any large scale system such as Bioinformatics,
Computational Sciences, and Computational Fluid
Dynamics. One popular way to build the high
performance computing system is to cluster
traditional personal computing together and then
apply grid computing technology such as globus grid
[6] or sun grid [7] to manage resources in the cluster
computing system.
However, most computing applications cannot be
transferred directly from traditional one processor
system to the cluster computing system. Several
considerations need to be taken care of, especially on
how to partition problem space and how to manager a
huge amount of distributed computing tasks. We
implement a distributed workload management
technique to alleviate these problems in our bacterial
common gene finding research and the details are as
follows in the next sections.
2. Methodology
The methodology for comparing gene sequence
tasks can be divided into four parts: data selection,
data extraction, comparison of gene sequences, and
distributed workload management. Query= gi|16077069|ref|NP_387882.1| alternate gene nam
dnaJ,
2.1 Data Selection dnaK [Bacillus subtilis]
(446 letters)
Genomic data is publicly available at the
National Center for Biotechnology Information Database: NC_000913.faa
(NCBI), also known as Genbank [8]. It is a part of 4279 sequences; 1,361,003 total letters
International Nucleotide Sequence Database Score E
Collaboration, which is comprised of the DNA Sequences producing significant alignments: (bits) Value
DataBank of Japan (DDBJ), European Molecular ref|NP_418157.1| DNA biosynthesis; init………….377 e-105
ref|NP_416991.1| putative DNA replication………… 71 1e-013
Biology Laboratory (EMBL), and the GenBank. ref|NP_415878.1| putative DNA replication………….30 0.25
The goal of our application is to find common
gene using all available bacterial genomic sequence Figure 2. Some BLAST results
from GeneBank, but initially as a prove of concept,
we use the data that consists of 5 bacteria, The example of pair-wise results is shown in
scientifically named as: Figure 2. All results will be stored in the pair-wise
1) Bacillus subtilis gene similarity database for further mining process as
2) Escherichia coli K12 shown in Figure 3.
3) Mycobacterium tuberculosis H37Rv
4) Pseudomonas aeruginosa PA01
5) Staphylococcus aureus subsp.aureus MW2 Bacterial
Pair-wise
comparation
Mining Common
Gene
Database Common Gene
Each bacteria specie has the number of genes BLAST Database

about 4,000-6,000. When downloaded from Figure 3. Common Gene Finding Process
GeneBank, they have their accession numbers as
{NC_000964,NC_000913, NC_000962, NC_002516, Suppose that we have n bacterial species, each
NC_003923}, respectively. has m genes. We can estimate the number of the
BLAST comparisons to be
2.2 Data Extraction n(n − 1) 2 (1)
Data Extraction is a process when relevant N= m
2
biological data is extracted from source database
Where
(GenBank), cleansed of redundant and unneeded
N is the total number of jobs in the system.
data, and then loaded into a biological database.
n is the number of bacteria.
From GeneBank’s genomic data, which contain in
m is the number of genes in a bacteria.
a plain text FASTA file format as shown in figure 1,
we extract gene sequences, their reference index and
For example, there are five bacterial genomic data
other useful information into out local database.
is shown in table 1.

>gi|16077069|ref|NP_387882.1| alternate gene name: dnaH, dn Table 1. Number of Genes

[Bacillus subtilis] Accession Number Number of Genes
MENILDLWNQALAQIEKKLSKPSFETWMKTKAHSLQG NC_000964 4112
GEELSIKFVIPQNQDVEDFMPKPQVKKAVKEDTSDFPQN
AKAYNPLFIYGGVGLGKTHLMHAIGHYVIDHNPSAKVV
NC_000962 3927
LLIDDIQFLAGKEQTQEEFFHTFNTLHEESKQIVISSDRPP NC_000913 4279
RIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALI NC_003923 2632
PKVITIKEIQRVVGQQFNIKLEDFKAKKRTKSVAFPRQIA
HEKISKLLADDEQLQQHVKEIKEQLK
NC_002516 5567

Figure 1. Example of gene sequence data
in FASTA format
2.3 Comparison of gene sequences
In this comparison step, we use gene sequence
comparison tool called BLAST, which is popular for
searching sequence similarity in sequences database
by a given query sequence.[8] The query sequences
can be protein sequences or DNA sequences.
If the average of genes in the bacterial is about
4,000 genes, the total number of comparison jobs is
10*(4,000)2 jobs. If the number of bacterial genomic
data is 128 (as they are seqvenied), the total number
of comparison jobs is
(128)(127)
4000 2
2
In another words, time process may be used more
than 1011 pair-wise comparing. If job uses the
processing time 0.001 second, the overall processing
time of comparison is 0.001x1011 = 108 second or
1,157 days or about 3 years. If we have more than
one computer machine that can perform comparison
task in parallel, this process can drastically reduce the
processing time.
2.4 Distributed Workload Management
The distributed workload management concepts
is to manage workload using cluster computing and
grid computing technology [6],[7].
Our preliminary cluster computing system
consists of 5 nodes. Each computing node is dual
Athlon MP1.8 1533 MHz with 512 MB of DDR
RAM. To speed up the data transfer, we exploit the
high bandwidth of the gigabit Ethernet technology. It
is shown in figure 4.
Figure 4. Cluster Computing System
To manage the workload computing, we use grid
engine to manage distributed resources. The grid
computing system is a collection of computing
resources such as distributed CPU resources,
distributed Disk I/O resources, and distributed
memory resources. It also provides queuing control
for a huge amount of job submitted. It is shown in
figure 5.
Job submitted
Grid Engine System
Cluster Computing Systems
CPU Disk I/O Memory
Figure 5. Grid Engine System
A job is submitted into the grid engine system
through a host, named, frontend-0. When the grid
engine receives the job, it assigns the status of job
submitted as ‘qw’ which means queue-wait. If
resources of cluster computing system are available,
the grid engine allocates the resources to the queued
jobs. The queued jobs’ status are changed as ‘r’
which means running. Then the running jobs use
resources of cluster computing nodes such as
compute-0-8, compute-0-9, and compute-0-10. When
the job is finished, the results are stored in Bio-
Database node, named, frontend-1.
There are three cluster computing nodes in the
system. For optimal performance of a dual processor
system, each node is assigned to run two independent
jobs. The available of queue space is called slot, thus
each cluster computing node in the system contains
two slots. There are six jobs which can be activated,
while other have non-activated or queued status.
k
S= ∑s
i =1
i (2)
Where
S is the total number of slot in the cluster
computing system.
s is the total number of slot in the ith node.
k is the total number of cluster computing node.
We build a script to monitor the queued slot and
submit a new job into grid engine system when any
slot becomes available. To monitor the queued slot,
we create a table to contain the status of job
submitted.
STATUS = {‘Q’,’P’,’C’}
Let
Q denoted Queue Process type.
P denoted Progress Process type.
C denoted Complete Process type.
When the status of job submitted on grid engine
system is ‘qw’, the STATUS of job submitted is
updated as ‘Q’. If status of job submitted on grid
engine system is ‘r’, the STATUS of job submitted is
updated as ‘P’. If status of job submitted on grid
engine system is completed, the STATUS is updated
as ‘C’.
3. Experimental Results
The dataset to test our system is defined by three
workloads are shown in table 2:
 Table 2. Three workloads The processing time of the three workloads on the
Total number of Bacterial comparison 6-cpu system is shown in table 4:
Bacterial species
Workload 1: NC_000962<->NC_000913 Table 4. Processing time by three workloads
3 bacteria NC_000962<->NC_000964 No. Workload t1(s) tc (s) T (s)
{NC_000962, NC_000913<->NC_000964 Workload 1 3,415 1,180 2.8941
NC_000913, Workload 2 8,491 1,955 4.3432
NC_000964} Workload 3 11,970 2,478 4.8305
Workload 2: NC_000962<->NC_000913
4 bacteria NC_000962<->NC_000964 From the table 4, the plots representing the
{NC_000962, NC_000962<->NC_002516 results are shown in figure 6 and figure 7,
NC_000913, NC_000913<->NC_000964 respectively.
NC_000964, NC_000913<->NC_002516
NC_002516} NC_000964<->NC_002516 processing time of one-cpu
11000
Workload 3: NC_000962<->NC_000913 processing time of cluster system
10000
5 bacteria NC_000962<->NC_000964

Processing time (second)

9000
{NC_000962, NC_000962<->NC_002516
NC_000913 NC_000962<->NC_003923 8000

NC_000964, NC_000913<->NC_000964 7000

NC_002516, NC_000913<->NC_002516 6000

NC_003923} NC_000913<->NC_003923 5000

NC_000964<->NC_002516 4000
NC_000964<->NC_003923 3000
NC_002516<->NC_003923 2000

3 6 10
The processing time of pair-wise comparison on Number of bacterial comparison
one-cpu computer is shown in table 3: Figure 6. processing time of tc and t1
Table 3. Processing time of pair-wise comparison 5

Bacterial comparison Processing Time(s)

NC_000962<->NC_000913 1,240 4.5
NC_000962<->NC_000964 1,064
NC_000962<->NC_002516 2,021
Speed-up time (second)

NC_000962<->NC_003923 704 4

NC_000913<->NC_000964 1,115
NC_000913<->NC_002516 1,637
3.5
NC_000913<->NC_003923 798
NC_000964<->NC_002516 1,418
NC_000964<->NC_003923 863 3
NC_002516<->NC_003923 956

To compare the processing time of sequence 2.5

3 6 10
similarity searches on one-cpu computer to the Number of bacterial comparison

processing time of three-computer, 6 cpu, we defined Figure 7. speed-up time from 1-cpu to
the speed-up equation as follows: a cluster system
t i1
T= ; for i = 1,2,3 (3) 4. Conclusion and Future Work
t ic
From the preliminary results, the grid computing
Where technology can reduce the overall processing time on
T is the speed-up time from t1 to tc bacterial common gene finding application. For
t1 is the processing time of one-cpu computer at future work, experiments will be conducted on more
the ith workload. bacterial species and more computing nodes will be
tc is the processing time of 6-cpu computer at the applied. We also plan to use other data analysis and
ith workload. data mining techniques on the bacterial comparative
genomic application.
5. Acknowledgement
This study has been funded by RD-C2 section of
NECTEC. Special thanks to Shobhna S. of RD-C4
section, who troubleshooted many Sun grid
problems.

6. References
[1] Vladir Filkov, Steven Skiena, Jizu Zhi, “Analysis
Techniques for Microarray Time-Series Data,”
International Journal of Computational Biology,
Vol.9,No.2,2002, pp 317-330
[2] Jiawei Han, Micheline Kamber, Data Mining: Concepts
and Techniques, Morgan Kaufmann, 2001
[3] Jaiwei Han, How Can Data Mining Help Bio-Data
Analysis, Workshop on Data Mining in Bioinformatics
with SIGKDD02 Conference, 2002
[4] Jack Y. Yang, Okan K. Ersoy, Mary Qu Yang, Gene
Finding and Protein Function Determination Using Protein
Phylogenetic Profiles and Computational Intelligence,
Intelligent Engineering Systems Through Artificial Neural
Networks, Vol.12, 2002, pp 735-740
[5] Lev A Soinov, Maria A Krestyaninova, and Alvis
Brazma, Towards reconstruction of gene networks from
expression data by supervised learning, Genome Biology,
2003, http://genomebiology.com/2003/4/I/R6
[6] Globus Project, University of Chicago,
http://www.globus.org/
[7] Grid Engine, Sun Microsystems,
http://gridengine.sunsource.net/
[8] GenBank, National Center for Biotechnology
Information, http://www.ncbi.nlm.nih.gov/