International Journal of Computer Science and Information Security (IJCSIS),
Vol. 14, No. 12, December 2016
Database Search, Alignment Viewer and
Genomics Analysis Tools: Big Data for
Bioinformatics
Muhammad Atif Sarwar Abbas Rehman
Department of Computer Science Department of Computer Science
COMSATS Institute of Information COMSATS Institute of Information
Technology Technology
Sahiwal, Pakistan Sahiwal, Pakistan
atifsarwar@ciitsahiwal.edu.pk abbasrehman@ciitsahiwal.edu.pk
AbstractAdvancement in the sequencing technology has
resulted in the production of large amount of omics data in
short time. Traditional bioinformatics tools cannot cope with
the rate of production of such huge amount of data. So, new
tools need to be developed and existing tools need to be
improved. New researchers, developers and Bioinformaticists
face difficulty in selecting the appropriate tool for Analysis of
data or for making improvements in the tools. This paper
presents a comprehensive survey on the availability of
bioinformatics tools, purpose of different tools, programming
languages used for development of different tools and data
formats used for different tools. It also presents either a tool
has been enhanced to be used on Big Data platform or not.
I. INTRODUCTION
With the passage of time, new approaches and
technologies has been developed because massive
amount of data is available. A large amount of data is
available in many fields such as Electrical, Mechanical,
Electronics, Mathematics, Management Sciences,
Computer Science and Bioinformatics. A tool of stack is
provided for every field of data that will help us to
analyze and store data.
Recently, the term Big Data has been introduced
which denotes the huge amount of data in Computer
Science field. This large data needs to be analyzed, stored
and managed for example, data of Facebook, Yahoo,
This paper was submitted for review on 14 December 2016.
Muhammad Atif Sarwar is with department of computer Science,
COMSATS Institute of Information Techology, Sahiwal, 57000
Pakistan (e-mail:atifsarwar@ciitsahiwal.edu.pk).
Abbas Rehman is with department of computer Science, COMSATS
Institute of Information Techology, Sahiwal, 57000 Pakistan
(e-mail:abbasrehman@ciitsahiwal.edu.pk).
Javed Ferzund is with department of computer Science, COMSATS
Institute of Information Techology, Sahiwal, 57000 Pakistan
(e-mail:jferzund@ciitsahiwal.edu.pk).
317
Javed Ferzund
Department of Computer Science
COMSATS Institute of Information
Technology
Sahiwal, Pakistan
jferzund@ciitsahiwal.edu.pk
Twitter and Walmart. Big Data has characteristics of 5
Vs such as Veracity (amount of consuming data),
Velocity (processing of data), Variety (types of data),
Volume (amount of data) and Potential Value (giving
value to data). Potential Value is very important for future
thoughts and for planning of data. Big Data flow includes
two types of processing such as real time (new SQL) and
batch (based on analytics). Performance is the big
challenge for Big Data. Many tools and systems are
available which manage the Big Data for example
Hadoop (distributed management System).
At the same time, Bioinformatics data has been also
produced in large amount such as Genomics, Proteomics,
RNA, DNA, and Motif Finding. A lot of data will be
produced for Sequence Alignment (multiple and
Pairwise) from RNA, DNA and Proteins. Some data will
be produced for their relationships such as Protein to
Protein, Gene to Disease, Disease to Gene, and Gene to
Protein. Some important data will be available for
database search. NGS (Next Generation Sequencing) has
produced a lot of sequencing data.
In upcoming Era, this data will increase in large
amount day by day. All of this Bioinformatics data is
required to be analyzed and stored in a well-organized
way. For this purpose, an open source Apache Hadoop
system had been designed for large distributed storage
and exploration of large data. This will give advantages
of fault tolerance, security and efficiency. Hadoop
consists of HDFS (Hadoop Distributed File System),
MapReduce (a programming paradigm) and many tools
built on it like HBase, Hive, Pig, Zookeeper etc.
HDFS (Hadoop Distributed File System) is
distributed system for data storage and data processing
with many clusters by programming help. It contains
name node and data node (like master slave relationship).
HBase contains read write data access with ACID
properties. Hive is data warehouse system with HQL
(Hive Query Language) interface. It also provides the
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 International Journal of Computer Science and Information Security (IJCSIS),
Vol. 14, No. 12, December 2016
facility of Hive data units such as Partition, Bucket and
Table.
Hadoop MapReduce is system for parallel processing
of large data using simple programing. It contains Map
and Reduce tasks with job and task tracker (like master
slave relationship). Apache also provides Spark
framework for Analysis of large data with the help of
Transformations, RDD (Resilient Distributed Datasets),
Actions and Caching. It includes many Built-in libraries
for multiple purposes. Apache Platform has advantage of
best Performance than Hadoop MapReduce.
Many Bioinformatics tools are designed for
processing and analysis of Bioinformatics data such as
RNA, DNA, Genomics and Proteomics. These tools are
not Scale when this huge amount of data is concerned. To
remove this bottleneck, these tools are implemented in
Hadoop Platform for processing of large Bioinformatics
data. Some tools are implemented in Hadoop for
Alignment viewers, some for database searching, some
for Genomic Analysis, Mostly Bioinformatics tools are
implemented in MapReduce or in Spark framework.
Hadoop modules support many languages such as
Java, Python, and Scala etc. Bioinformatics tools are
implemented in specific language in MapReduce or
Apache Spark framework. Some tools are implemented
in Java, some in Python, some in Scala and some in
C++/C# language. When these tools are implemented in
MapReduce then mostly Java language is used for
processing. When these tools are implemented in Spark
then Scala, Java and Python are mostly used languages.
It is most important opinion what Data Format will be
selected for the storage of large Bioinformatics data.
Focus of Data Format is compulsory when
Bioinformatics tools are implemented in MapReduce or
Spark framework. Some Data Formats are performing
well with small datasets but when Bioinformatics data is
large then these Formats are not scale. There are different
Data Formats for large data storage of Database
Searching, Alignment viewer editor.
The objectives of this survey are:
To explore all tools in the Bioinformatics
domain
To explain specific implementation platform
for these Bioinformatics tools
To recognize specific implementation
language for specific tool
To understand Data Format for storageand
analysis of large data in MapReduce or
Spark framework
Rest of this survey is organized as follows: Section 2
describes the related work in this field. Section 3 presents
the available Bioinformatics Tools and their
characteristics in terms of category of tools,
318
implementation language, data format support and
implementation for Big Data. Section 4 presents a brief
discussion and finally conclusion is presented in Section
5.
II. RELATED WORK
The larger sizes of data has [1] been Analyzed and
executed with distributed computing on computer
clusters. The rapidly growing data quantities, for
example, DNA sequencing, and new methods to data
analysis are required. Hadoop is used for data processing
that is a collection of software designed especially for Big
Data, with the basic working of the Hadoop Distributed
File System and Hadoop MapReduce scalable distributed
computing platform and Apache Spark. This effort tells
about the working of Hadoop MapReduce and Apache
Spark for the bioinformatics data. The growth of
bioinformatics data is so fast that it can only be stored and
manipulated with the technology of Hadoop MapReduce
and Apache Spark and HDFS environment. Thus new file
formats are being developed to better cope with the needs
of modern and future Big Data sets. This work analyses
the current state of the art tools in the world of
bioinformatics and their implementation for Big Data
Platforms.
Schatz et al. have [2] developed the CloudBurst that
is used for the genome mapping process. CloudBurst
provides parallel short-read mapping method to boost the
measurability of reading largest sequencing data. Many
new tools have been developed by CloudBrust team to
support the field of biomedical, for example Crossbow
used for the recognizing single nucleotide
polymorphisms (SNPs) from sequencing data and
Contrail use for the aggregation giant genomes.
Pandey et al. have designed the DistMap toolkit [3]
on a Hadoop cluster for distributed short-read mapping.
DistMap aims to extend the support of various styles
of mappers to cover a wider variety of sequencing
applications. The nine supported mapper types include
SOAP, STAR, GSNOP, BWA, Bowtie, Bowtie2,
Bismark, BSMAP and TopHat. A DistMap is integrated
with mapping workflow, which could be run with simple
command.
OConnor et al. have built the SeqWare that could [4]
be a query based engine designed on the Apache HBase
database to assist bioinformatics researchers access
large-scale whole-genome datasets. The interactive
interface to integrate the genome tools and browser was
created by SeqWare team. During a prototyping analysis,
the 1102GBM and U87MG tumor database were laden,
and the team match the HBase back end and the Berkeley
DB and for exporting variant and loading data capabilities
Lewis et al. have made the Hydra that is a search [5]
engine for scalable proteomic search which is built on the
Hadoop-distributed computing framework. Hydra gives
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 International Journal of Computer Science and Information Security (IJCSIS),
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the software bundle for processing spectra and largest
peptide databases, with the implementation of distributed
computing framework that supports massive quantities of
spectrometry data for scalable search. The Hydra divided
the proteomic search into two steps: (1) scoring the
spectra and retrieving the data and (2) generating a
peptide database.
Van der Auwera et al. have launched the Genome
Analysis Toolkit (GATK) designed [6] to support large-
scale DNA sequence Analysis based upon the
MapReduce programing framework. GATK backings
several data formats, including binary alignment/map
(BAM), SAM files, dBs and Hap Map. The GATK toolkit
prepares two modules traversal and walker. The traversal
modules read sequencing data into the system and
provide related references to the data. The walker
modules provide analytics outcome from the data. GATK
has been used for the 1000 Genomes Projects and Cancer
Genome Atlas.
Van der Aurar et al. have introduced Myrna that is a
[7] cloud-based computing pipeline used to calculate
difference in gene expression for very large transcript
RNA sequencing datasets. RNA sequence data are m-
sequencing reads derived from mRNA molecules. Myrna
supports several functions for RNA-seq Analysis,
including normalization, reads alignment, and statistical
modeling in an integrated pipeline. Myrna returns
differential expression of genes into the form of P-value
and q-value and analytical plot of those genes. This
system was tested on the Amazon Elastic Compute Cloud
(Amazon EC2) using 1.1 billion RNA-seq reads, and the
results show that Myrna can process data in less than two
hours and the cost of the test task was around $66.
Chung et al. proposed the CloudDOE, a software [8]
tool set that offers a user friendly interface to implement
the Hadoop cloud because the Hadoop platform in itself
is too complex to be handled by a user that has no
expertise in computer science or some other technical
skills. This tool is very simple to be handled by a layman
and it uses MapReduce to analyze very complex
procedures such as the throughput of sequences in
bioinformatics data. This tool is a support for scholars and
researchers to easily configure Hadoop cloud to study
different aspects of Bioinformatics data.
Robinson et al. presented the SAMQA, a special [9]
toolkit designed to find errors in genomic data and it
guarantees that the sequencing data must fulfill the
significant quality measures. The tool was intentionally
developed for the National Institutes of Health Cancer
Genome Atlas for an automatic detection of errors and
thus generating a log file of these errors. The tool uses
some technical tests to identify abnormalities in genomic
data such as invalid CIGAR value or sequence
alignment/map (SAM) format error. For the same
biological data set of approximately 23GBs in size, a
comparison of SAMQA on a single-core server and of
319
Hadoop on cluster has shown that Hadoop performs 80
times speedily than SAMQA.
Angiuoli et al. designed the CloVR, a sequence [10]
analysis tool distributed over a virtual machine. This tool
is an equal support for both cloud systems as well as
personal desktop systems to process the sequencing data
thus removing all the hazards to analyze large datasets.
There are many other bioinformatics workflows that
incorporate virtual machines including metagenome,
whole-genome, and 16S rRNA-sequencing Analysis.
To check the portability of CIoVR for local host and
cloud platform, this tool is tested against a local machine
(4 CPU, 8 GB RAM) and on the Amazon EC2 cloud
platform (80 CPU). And the results concluded that
CIoVR is potable on both platforms.
Oehmen et al. proposed the bioinformatics tool that is
used for parallel five BLAST calculations (blastn, blastp,
tblastn, tblastx and blastx) [11] on large and small scale
systems in genome and protein sequence on
multiprocessor environment. ScalaBLAST 2.0 provides
dynamic data partitioning (fault resilience properties) and
does not require pre-formatting (repeated same datasets)
than ScalaBLAST 1.0 and mpiBLAST that contains
single processor. It is implemented using NCBI BLAST
C toolkit and depends on MPI library. The input file in
the FASTA format and output formats (standard
pairwise, tabular and tabular with headers).
Michael C. Schatz introduced the BlastReduce, a [12]
parallel seed-and-extend alignment algorithm (includes
three MapReduce cycles) that takes DNA NGS data
(short reads) and then align or map these read to reference
genome (database of specific specie) on Hadoop
MapReduce paradigm that support parallel execution.
Landau-Vishkin alignment algorithm reduces this
infeasibility. BlastReduce is much faster than BLAST
and reduce the execution time. It is implemented in Java
with Hadoop and compatible with cloud computing. Like
BLAST, BlastReduce uses seed-and-extend technique
and Unlike BLAST, BlastReduce uses Landau-Vishkin
algorithm. Their performance shows that BlastReduce is
scalable to large sets of read and highly speed up.
III. TOOLS FOR BIOINFORMATICS
There are many Bioinformatics tools that are used for
analysis of small and large datasets. Every tool performs
specific function. Different tools are used for alignment
viewer editor, database search and genome analysis.
These tools require the data to be stored in a specific
format for any kind of analysis. These tools are built using
different programming languages.so, it is important to
know the specific language in order to customize the
tools. The skills in a programming language are more
helpful when extending these tools for Hadoop
MapReduce or Apache Spark framework.
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 International Journal of Computer Science and Information Security (IJCSIS),
Vol. 14, No. 12, December 2016

A. Alignment Viewers/Editors sequence analysis of biological data such as nucleotide or

In this category, a number of tools are available which
provide quicker, easier and user friendly interfaces for the
The Ale (emacs plugin) is implemented in lisp and c,
AliView in Java, Base By Base in Java and BioEdit is
implemented in Python. Java, C++ and Python are used
by BioNumerics, C is used for BoxShade, C++, Java and
Perl is used for the implementation of CINEMA. CLC
viewer is implemented in C, C++ and python, ClustalX
viewer is implemented in BioPython. Table 1 presents the
tools available for alignment view and editing.
Every tool has the specific data format for the storage
and analysis purposes. Ale (emacs plugin) supports the
GenBank, EMBL, Fasta and Phylip. AliView tool
protein sequences. Many programming languages have
been used for the implementation of the alignment
viewers or editors.
supports the Nexus, MSF FASTA PHYLIP, and Clustal.
Base-by-Base supports the EMBEL, Genbank, Base-by-
base files, Clustal, BioEdit support data format.
BioNumerics uses the Genbank, and Fasta format for the
storage and Analysis of data.
Some of the alignment viewer/editor tools are
implemented in Apache Spark and Hadoop MapReduce
framework for the Big Data Analysis and the sequence of
biological data. DNASTAR Lasergene Molecular
Biology Suite and Maestro are implemented in Hadoop
MapReduce framework.

Table 1: Overview of Alignment Viewer/Editor that use MapReduce and Spark Framework

Name Language Data Format MapReduce Spark

Lisp, C, [13]
Ale (emacs plugin) GenBank, EMBL, Fasta and Phylip NO NO
Java
AliView [14] Nexus, MSF Fasta Phylip, and Clustal NO NO
[15]
Java EMBEL,Genbank, Base-by-base files,
Base-By-Base NO NO
[16] Clustal
Python, Java, C, C++, C# and Perl
NBRF/PIR, Phylip 3.2, Phylip 4,
BioEdit [17] [18], [19] NO NO
Genbank, Fasta
C++, Python
BioNumerics [20] Genbank, Fasta NO NO
[21]
READSEQ, ALN format as written by
C
BoxShade [22] Clustal W, NO NO
[23]
PILEUP,
C++, Python , Java, Perl Nexus, MSF, Clustal, Fasta Phylip, PIR,
CINEMA [24] NO NO
[25] PRINTS
CLC viewer [26] C/C++ and Python [27] Many NO NO
ClustalX viewer Biopython
Nexus, MSF, Clustal, Fasta Phylip NO NO
[28] [29]
Cylindrical
Java INSDSet, GFF3, ClustalW, Blast, XML,
BLAST Viewer NO NO
[31] proprietary XML,
[30]
Perl, R
DECIPHER Fasta Fastq, GenBank NO NO
[32]
Discovery Studio C, C++, Java SPT, SEQ, PDB, EMBL, HELM,
NO NO
[33] [34] Clustal, GDE, FASTA BSML, GB
Perl
DNASP [35] Fasta Nexus, Mega, Phylip NO NO
[36]
DNASTAR
Lasergene C/C++/Python ABI, DNA Multi-Seq, Fasta GCG YES
NO
Molecular Biology [37] Pileup, GenBank, Phred [38]
Suite
Java
FLAK Fasta NO NO
[39]

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Python, C++, C
Genedoc [40] MSF NO NO
[41]
Perl/Python/Java/C++/C
Geneious Fasta NO NO
[42]
Integrated Genome
Perl, C/C++ and Java
Browser (IGB) BAM, Fasta PSL NO NO
[44]
[43]
C++ and Java MSF,ClustalW, ,Nexus, PIR, Phylip,
IVistMSA [45] NO NO
[46] GDE,
Java BLC, PIR, Stockholm, MSF, Clustal,
Jalview 2 [47] NO NO
[48] Fasta PFAM
Java FASTA MSF, Clustal, Phylip, Newick,
JEvTrace [49] NO NO
[50] PDB
Javascript
JSAV [51] An array of JavaScript objects NO NO
[52]
Java YES
Maestro [53] Clustal, Fasta PDB NO
[54] [55]
C++
MEGA [56] FASTA Clustal, Nexus, Mega, etc NO NO
[57]
MSAReveal.org
Java [59] Fasta NO NO
[58]
Multiseq (vmd C++ [61]
Fasta PDB, ALN, Phylip, Nexus NO NO
plugin) [60]
MView [62] Perl Clustal, HSSP, Fasta PIR, MSF, Fasta
NO NO
[63] search, Blast search
Java
PFAAT [64] Nexus, MSF, Clustal, Fasta PFAAT NO NO
[65]
Ralee (emacs
Perl
plugin for RNA Stockholm NO NO
[67]
[66] )
Java
S2S RNA editor Fasta RNAML NO NO
[68]

C, C++ Nexus, MSF, Clustal, Fasta Phylip,

Seaview [26] NO NO
[69] MASE

Objective C NBRF/PIR,Nexus, Clustal, GDE,

Seqotron [27] NO NO
[70] Stockholm, flat, MEGA, Fasta
Sequilab [71] C++ Fasta NO NO
C, C++, Perl
Sequlator [72] MSF NO NO
[73]
Javascript
SnipViz [74] Fasta newick NO NO
[75]
C, C++ PDB, Embl, Pfam, Nexus, Fasta
Strap NO NO
[76] Clustalw, MSF
Fastq,GFF3, SAM, BAM, ACE, AFG,
Tablet [77] Java NO NO
Fasta MAQ, SOAP2,
Fasta Fastq, ClustalW, Stockholm,
UGENE C++, Qt ABIF, SCF, Newick, GenBank, EMBL, NO NO
PDB, MSF, GFF
C++ [78]
VISSA sequence Clustal, Fasta NO NO
Python
DNApy Fasta Fastq, GenBank NO NO
[79]
Alignment Javascript
Fasta NO NO
Annotator [80] [81]

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B. Database Search
Many new tools are available for searching in protein
and nucleotide sequence databases. With the
advancement in technology, many tools have been
developed for database search. These are implemented in
different languages like C, C++, C#, Java, Perl, Python,
CUDA C++ and PTX assembly language, Java, Android,
Objective-C, and Ruby. These tools include BLAST, CS-
BLAST, CUDASW++, DIAMOND,
GGSearch/GLSearch, Genoogle, and HMMER. A list of
the available tools in this category is presented in Table
2.
The Database Search tools support different formats
for querying the stored data. The supported formats
include FASTA bare sequences, identifiers, Genbank,
FASTQ, EMBL, Genbank, CLUSTAL, Stockholm,
A2M, A3M, EMBL, MEGA, GCG/MSF, PIR/NBRF and
TREECON. Some of these tools have been implemented
on Hadoop MapReduce and Apache Spark. Tools like
BLAST, DIAMOND, HMMER, HHpred/ HHsearch,
ScalaBLAST are implemented on Hadoop MapReduce
and Apache Spark Framework.

Table 2: Overview of Database Search tools that use MapReduce and Spark Framework

Name Sequence Type Language Data format MapReduce Spark

BLAST Nucleotide or C, C++, C#, Java, Perl and Fasta bare sequences, YES [12]
NO
[82] protein sequence Python. identifiers, Genbank

CS-BLAST Protein sequence C++ Fasta NO NO

CUDASW CUDA C++ and PTX Fasta

Protein sequence NO NO
++ [83] assembly languages
Java, Android, Objective- NO
DIAMON Fasta Fastq
Protein sequence C, Python and C++ NO
D
[84]
FASTA Nucleotide or Python, Ruby, and Perl Fasta
NO NO
[85] protein sequence [86]
C/C++
GGSearch/ Fasta
Protein sequence BioPerl, BioPython NO NO
GLSearch

Nucleotide or Fasta
Genoogle Java NO NO
protein sequence
HMMER Nucleotide or Fasta EMBL, Genbank YES
C NO
[87] protein sequence [88]
Fasta , A2M, GCG/MSF,
HHpred/ A3M,PIR/NBRF,EMBL,
Protein C++ YES [88] NO
HHsearch MEGA, Clustal

Sequence
C++, Java Fasta
KLAST similarity search NO NO
tool
Nucleotide or C/C++ Fasta
USEARCH NO NO
protein
Fasta
Nucleotide or
Parasail Python or C Fastq NO NO
protein

C++, Java, R Matlab,

PSI- Fasta
Protein Python NO NO
BLAST

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PHYLIP, GCG,
PSI-Search Java
Protein UniProtKB, PIR, NO NO
[89]

ScalaBLAS Nucleotide or Fasta YES

Java, C++, Python [90] YES [91]
T protein [92]
Nucleotide/ Java Fasta
Sequilab NO NO
Peptide
Nucleotide or Fasta
SAM Java YES NO
protein

Nucleotide or C++ Fasta

SSEARCH NO NO
protein
C++ Fasta
SWAPHI Protein NO NO
/FASTQ
SWAPHI- DNA sequence file
DNA C/C++ NO NO
LS
C Fasta
SWIMM Protein NO NO

Nucleotide or C++ Fasta

SWIPE NO NO
protein

C. Genomics Analysis
Tools in this category are used for analysis of
nucleotide or peptide sequences. Different programming
languages are used for implementation of genome
analysis tools. Java language is used by ACT, FLAK,
Mauve, Mulan, Sequero and Shuffle-LAGAN. Perl is
used by BLAT, Sim4/ SIBsim4 and SLAM tools. R is
used by DECIPHE R tool for implementation.
FORTRAN is used by GMAP tool for implementation.
C++ is used by GMAP, Splign, Mauve, Sequilab,
Shuffle-LAGAN and sim4 tools for implementation.
FORTRAN is used by GMAP tool for implementation. C
is used by GMAP, PLAST-ncRNA, Sequilab, Shuffle-
LAGAN, Sim4 and SLAM tools for implementation.
Python is used by MGA, Multiz, PLAST-ncRNA and
Sequilab tools for implementation. Ruby language is used
by the SLAM tool. Table 3 presents the tools available
for Genomics Analysis.
Every tool supports specific format for efficient data
storage. EMBL format is used in ACT and Sim4 tools for
data storage. EMBL format is used in ACT and Sim4
tools for data storage. GENBANK format is used in ACT,
Mauve, MGA, Mulan and Sim4 tools for data storage.
GFF format is used in ACT tool for data storage. FASTA
format is used in ACT, BLAT, DECIPHE R, GMAP,
Splign, Mauve, Mulan, Multiz, PLAST-ncRNA,
Sequilab, Shuffle-LAGAN, Sim4 and SLAM tools for
data storage. Multi-FASTA format is used in Mauve tool
for data storage. Bare format is used in Mulan and Multiz
tools for data storage. Fastq format is used in PLAST-
ncRNA tool for data storage.
Some of these tools like BLAT, GMAP and MGA are
implemented in Hadoop MapReduce framework for
genome Analysis. Specific format is used in the
implementation of BLAT, GMAP and MGA tools for
input data in Hadoop MapReduce or Apache Spark
framework.

Table 3: Overview of Genomics Analysis tools that use MapReduce and Spark Framework

Name Sequence Type Language Data Formats MapReduce Spark

EMBL, GENBANK
ACT (Artemis
Java GFF, Fasta
Comparison Tool) Nucleotide NO NO
[93]
Fasta
BLAT Nucleotide Perl YES [12] NO

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R NO
DECIPHER Nucleotide Fasta NO
Java
FLAK [94] Nucleotide Fasta NO NO
Fasta
Fortran, C and C++ YES [96]
GMAP [95] Nucleotide NO

C++ Fasta
Splign [97] Nucleotide NO NO

Java Fasta Multi-Fasta

Mauve [98] Nucleotide C++ GenBank NO NO

Genbank
Python
MGA [99] Nucleotide NO NO

Java Fasta Bare,Genbank

Mulan Nucleotide NO NO
Python Bare, Fasta
Multiz Nucleotide NO NO
Fasta Fastq
PLAST-ncRNA Nucleotide C, Perl, Python NO NO
Java
Nucleotide or Fasta
Sequerome NO NO
peptide
Fasta
C, C++,
Nucleotide or
Sequilab Python, SIMD NO NO
peptide
dynamic
C, C++, Java and Perl Fasta
Shuffle-LAGAN Nucleotide NO NO
C/C++
SIBsim4 / Sim4 Embl, Fasta GenBank
Nucleotide Perl NO NO

C ,Perl and ruby

Fasta
SLAM Nucleotide NO NO

IV. FUTURE OF BIOINFORMATICS TOOLS
Bioinformatics research data is very large in size,
complex in nature and critical for results. Conventional
research methods exhibit very greater time complexity
while analyzing results and very high space complexity
while storing such massive datasets thus requiring
systems with tremendously high processing capabilities.
For example, the NCIs The Cancer Genomics Atlas
(TCGA) dataset alone is 2.5 Petabytes and it would take
23 days to even download this dataset even with industry
standard internet speeds. So instead of introducing such
highly capable machines the concept of cloud computing
has taken the place. To handle large, complex and
distributed data of bioinformatics it is economical to
process datasets across the cloud. Cloud computing is
beneficial for big data analytics because it would
distribute data load across physically distant machines
thus improving efficiency, saving money and avoiding
single points of failure. Also the traditional bioinformatics
data analysis tools based on R, Perl, or python do not meet
the requirements to handle such huge datasets. So there is
a need to use different tools according to the nature of
datasets involved and the type of queries or results to get
insights of that data structures. It is a shift from data
generation to data analysis now.
The main goal to use statistics, machine learning
algorithms and data mining techniques to identify,
compile, analyze and visualize biological data structures
is to make new models that may help in epidemic disease
analysis, understanding evolution, matching genomics,
suggesting medicine, providing health care information
and predicting metabolomics processes. The main
purpose is to introduce and implement standard protocols
while analyzing huge bioinformatics data using modern
computer science techniques that will tackle the

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 International Journal of Computer Science and Information Security (IJCSIS),
Vol. 14, No. 12, December 2016
complexity in nature of data and combine data across the
cloud from distributed resources. Now the need is to fuse
robust, efficient, quantitative, accurate and precise data
visualization algorithms in previously implemented tools
of biological and biomedical fields to target all four Vs
of big data: volume of data, velocity of processing the
data, variability of data sources, and veracity of the data
V. CONCLUSION
NGS (Next Generation Sequencing) plays an
imperative role in the Bioinformatics field. There are
many tools exists which are implemented in Hadoop
MapReduce and Apache Spark framework. These tools
are implemented using specific language like C, C++,
Python, Scala and Java. Bioinformatics domain consists
of DNA, Protein, Genomics and RNA data. When this
data is stored in BI (Bioinformatics) tools then specific
data format will be used like GenBank, EMBL, Fasta
Fastq and Phylip 4 etc. When Bioinformatics data are
store in Hadoop MapReduce or Spark framework,
specific data format will be used such as Avro, Sparse
vector, (key, value) pair and Sequence file etc.
Alignment viewers/editors Tools implemented in
Hadoop MapReduce and Spark framework. We can
implement Alignment viewers/editor tools such as Ale,
AliView, Base by Base, BioEdit, BioNemerics,
BoxShade, CLC Viewer, DnaSP, FLAK, Genodoc,
Jalview 2, JSAV, JEvTrace, Mega, PFAAT, Seaview,
Sequilab, Snipviz, Strap, Tablet, DNApy and UGENE in
Hadoop MapReduce Platform. These tools can also
implement in Apache Spark framework. Alignment
viewer/editor tools such as DANASTAR and Maestro
have implemented in Hadoop MapReduce platform.
Database search also play a vital role in
Bioinformatics. Like Alignment viewer/editor tools,
database tools implemented in Hadoop MapReduce and
Apache Spark. We can implement Alignment database
tools such as CS-BLAST, FASTA GLSearch, Genoogle,
KLAST, Parasail, PSI-Search and Sequilab in Hadoop
MapReduce Platform. These tools can also implement in
Apache Spark framework. Database tools such as
BLAST, DIAMOND, HMMER, HHSearch and
ScalaBLAST have implemented in Hadoop MapReduce
platform. ScalaBLAST have implemented in Apache
Spark framework.
Genome Analysis consist of genes and microarray
data. Gene-to-Disease relationship show a significant role
in Genome Analysis. . Like Alignment database tools,
Genome Analysis tools implemented in Hadoop
MapReduce and Apache Spark for Bioinformatics
datasets. We can implement Genome Analysis tools such
as ACT, DECIPHE R, FLAK, Splign, Mauve, Mulan,
Multiz, Sequilab and SLAM in Hadoop MapReduce
Platform. These tools can also implement in Apache
Spark framework. Genome Analysis tools such as BLAT,
GMAP and MGA have implemented in Hadoop
MapReduce platform.
325
quality. This thing will ultimately help biological
scientists, pharmacists, patients, customers and
companies.
Like Multiple Sequence Alignment, Pairwise
Sequence Alignment tools implemented in Hadoop
MapReduce and Apache Spark for Bioinformatics
datasets. We can implement these tools such as ACANA,
AlignMe, CUDAlign, DNADot, DOTLET, FEAST, G-
PAS, LALIGN, mAlign, MUMer, Needle, NW, Path,
PyMOL, SEQALN, SIM, GAP, NAP, LAP, SSEARCH,
Water and YASS in Hadoop MapReduce Platform. These
tools can also implement in Apache Spark framework.
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327 https://sites.google.com/site/ijcsis/
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 International Journal of Computer Science and Information Security (IJCSIS),
Vol. 14, No. 12, December 2016

Muhammad Atif Sarwar is a fields. Currently, he is leading the Big Data Analytics
Lab Engineer at Department of Research Group at COMSATS Institute Sahiwal.
Computer Science, COMSATS
Institute of Information
Technology Sahiwal, Pakistan.
He received BS (CS) degree
from COMSATS Institute of
Information Technology Sahiwal, Pakistan in 2015.
Currently, he is a scholar of MS (CS) session 2015-
2017 in COMSATS Institute of Information
Technology Sahiwal, Pakistan. His main research
interests include Big Data Analytics and Machine
Learning. Particularly, he is interested in applications
of Big Data in the Bioinformatics field. Currently, he
is working with the Big Data Analytics Research
Group at COMSATS Institute Sahiwal.

Abbas Rehman is a Lab

Engineer at Department of
Computer Science, COMSATS
Institute of Information
Technology Sahiwal, Pakistan.
He received MCS degree from
COMSATS Institute of
Information Technology Sahiwal,
Pakistan in 2015. Currently, he is a scholar of MS (CS)
session 2015-2017 in COMSATS Institute of
Information Technology Sahiwal, Pakistan. His main
research interests include Big Data Analytics and
Machine Learning. Particularly, he is interested in
applications of Big Data in the Bioinformatics field.
Currently, he is working with the Big Data Analytics
Research Group at COMSATS Institute Sahiwal.

Dr. Javed Ferzund is an

associate professor at
Department of Computer
Science, COMSATS Institute
of Information Technology,
Sahiwal, where he served as
Head of Department from
2013-2015. He received PhD
degree from Graz University of Technology, Austria
in 2009. His main research interests include Big Data
Analytics, Internet of Things and Machine Learning.
Particularly, he is interested in applications of IoT and
Big Data in the Agro-Informatics and Bioinformatics

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