COMPARATIVE SEQUENCE ANALYSIS OF LIPOXYGENASE OF SPECIES OF ASPERGILLUS AND FUSARIUM USING WEB-BASED BIOINFORMATICS TOOLS

CHAPTER ONE
INTRODUCTION
1.1 Bioinformatics
Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics is both an umbrella term for the body of biological studies that use computer programming as part of their methodology, as well as a reference to specific analysis “pipelines” that are repeatedly used, particularly in the fields of genetics and genomics. Common uses of bioinformatics include the identification of candidate genes and nucleotides (SNPs). Often, such identification is made with the aim of improved understanding of the genetic basis of diseases, unique adaptations, desirable properties (especially in agricultural species), or differences between populations. In a less formal way, bioinformatics also tries to understand the organizational principles within nucleic acid and protein sequences. Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, and protein structures as well as molecular interactions. Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s (Attwood et al, 2011).
The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques to achieve this goal. Examples include: pattern recognition, data mining, machine learning algorithms, and visualization. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interaction, genome wide association studies, and the modeling of evolution.
1.2 Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences (Mount, 2004). Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.
If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance (Henikoff, 2001). Although DNA and RNA nucleotide bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role.
1.2.1 Sequence alignment methods
Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. Calculating a global alignment is a form of global optimization that “forces” the alignment to span the entire length of all query sequences.
By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity (Polyanovsky et al., 2011). A variety of computational algorithms have been applied to the sequence alignment problem. These include slow but formally correct methods like dynamic programming. These also include efficient, heuristic algorithms or probabilistic methods designed for large-scale database search, that do not guarantee to find best matches.
1.2.2 Software used in Sequence Alignment
The software tools commonly used for general sequence alignment tasks include ClustalW2 and T-coffee for alignment, and BLAST and FASTA3x for database searching. Commercial tools such as Geneious and PatternHunter are also available. Alignment algorithms and software can be directly compared to one another using a standardized set of benchmark reference multiple sequence alignments known as BAliBASE (Thompson et al., 1999). The data set consists of structural alignments, which can be considered a standard against which purely sequence-based methods are compared. The relative performance of many common alignment methods on frequently encountered alignment problems has been tabulated and selected results published online at BAliBASE (Thompson et al., 1999). A comprehensive list of BAliBASE scores for many (currently 12) different alignment tools can be computed within the protein workbench STRAP.
1.2.3 Basic Alignment Search Tool (BLAST) analysis
The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription regulation regions in genomic DNA. Basic Local Alignment Search Tool is the tool most frequently used for calculating sequence similarity (Altschul et al., 1990). BLAST comes in variations for use with different query sequences against different databases. All BLAST applications, as well as information on which BLAST program to use and other help documentation, are listed on the BLAST homepage. This chapter will first describe the BLAST architecture—how it works at the NCBI site—and then go on to describe the various BLAST outputs. The way most people use BLAST is to input a nucleotide or protein sequence as a query against all (or a subset of) the public sequence databases, pasting the sequence into the textbox on one of the BLAST Web pages. This sends the query over the Internet, the search is performed on the NCBI databases and servers, and the results are posted back to the person’s browser in the chosen display format. However, many biotech companies, genome scientists, and bioinformatics personnel may want to use “stand-alone” BLAST to query their own, local databases or want to customize BLAST in some way to make it better suit their needs. Standalone BLAST comes in two forms: the executables that can be run from the command line; or the Standalone WWW BLAST Server, which allows users to set up their own in-house versions of the BLAST Web pages. There are many different variations of BLAST available to use for different sequence comparisons, e.g., a DNA query to a DNA database, a protein query to a protein database, and a DNA query, translated in all six reading frames, to a protein sequence database. Other adaptations of BLAST, such as PSI-BLAST (for iterative protein sequence similarity searches using a position-specific score matrix) and RPS-BLAST (for searching for protein domains in the Conserved Domains Database, Chapter 3) perform comparisons against sequence profiles. The best known of these outputs is the default display from BLAST Web pages, the so-called “traditional report”. As well as obtaining BLAST results in the traditional report, results can also be delivered in structured output, such as a hit table, XML, or ASN.1. The optimal choice of output format depends upon the application. The final part discusses stand-alone BLAST and describes possibilities for customization. There are many interfaces to BLAST that are often not exploited by users but can lead to more efficient and robust applications. Once BLAST has found a similar sequence to the query in the database, it is helpful to have some idea of whether the alignment is “good” and whether it portrays a possible biological relationship, or whether the similarity observed is attributable to chance alone. BLAST uses statistical theory to produce a bit score and expect value (E-value) for each alignment pair (query to hit).

Download Full Material-N5000

CHAPTER ONE

1.0                                  INTRODUCTION

1.1 Background of the Study

The field of information technology has improved tremendously in the past decade with the invention of all kinds of new technologies for example e-commerce, e-learning, e-business, and e- registration to mention a few.

In this technological era of education and doing business, information is considered to be an important asset for any academic institution. The availability of student’s data and feedback can help an educational institution to align its business processes according to the needs of its students and stakeholders. The effective management of these data can help institutions reach out directly to their students and stakeholders and also streamline its activities.

Commitments towards the success of tertiary education can be achieved through innovations such as updating of information, continuous enrolment, e-payment, and online student registration as well. This innovation approach helps pioneer many of the conveniences of students.

Many events have demonstrated that successful e-business is those that recognize the needs of their target users and match them with relevant contents. We are now in the age of knowledge is power and content is king. This phrase is often used in reference to any business conducted on the internet. People want to access product and services of an individual or corporation on a 24/7 basis. They also expect reliable, functional fast and user friendly services and any corporation that provides such services have higher success rates.

These benefits of e-business are also felt in the academic institutions. It can be applied in the areas of student’s online registration and payment of school fees. This system will offer among other things effective customer service and stream line supply chain management (the strategic management of distribution channels and the processes that support them). This system will have a site and will be accessed using any browser such as Internet explorer, Mozilla Firefox, Opera, Chrome etc.

This project work on the design and implementation of e-registration system on tertiary institution is aimed at the modern way of addressing the concerns raised by students, in order to maintain an efficient service delivery system. Such concerns raised are the manual handling of registration and student records, with also the overall view of improving efficiency in the registration process.

E-registration site can be accessed from anywhere with an internet connection, mostly these sites are portals. Pena-Lopez, (2009) describes a web portal as a site that functions as a point of access to information on the World Wide Web and portals present information from diverse sources. E-registration is a system that could easily manage its student body while also providing added bonuses, with its main goal being to ease the transfer of information. It simplifies the registration process through a web-enabled, user-friendly wizard and digitizes all supporting documents using intuitive process and tools. The education system requires a tremendous amount of data and documentation, and this e-registration solution allows institutions to focus less on processing paperwork and more on what matters most such as meeting the educational needs of their students by having a cost-efficient, secure registration process that allows for easy access to students files. Intranets and portals are supposed to provide an infrastructure through which end-users can gain effective access to information sources needed to assist in daily tasks such as effective decision making, planning and research (Brakel, 2003).

Many institutions in Nigeria have been somewhat quick to recognize the powerful transformational potential of portals and have developed and implemented their own. One of such is the portal of Federal University of Technology, Owerri, Nigeria. Broadly one could argue that an institution with increasing student numbers, operating in a society with an increasing desire for instant access to information, needs to carefully consider new ways in which it can interact more efficiently with its students (Brown 2000; Twigg and Obinge 1997).

At Imo State Polytechnic Umuagwo, just like the other polytechnics, students are enrolled to pursue a 2-year National Diploma academic program (ND), and a 2-year Higher National Diploma program (HND). Students must pass and obtain the minimum polytechnic admission requirements of the SSSCE/WASSCE examination in order to qualify for admission.

An enrolled student is expected to register and pay their school fees. In most cases, enrolling and having to register a new student involves some manual processes which delay processes for both the polytechnic and more especially the students.

Student’s registration is done by students mostly at a registration center. Students have to move physically to campus to complete the registration process. The following are the problems inherent with the current system.

1. Insufficient utilities in handling student’s registration.
2. Inability of students to remotely register and access their registration number immediately.
3. Students spend too much time in processing their registration and worse, this can only be done with their physical presence on campus.

The current system is outdated and can only be accessed through a clerk in the registration office/center. The new system will enable all students to access the system through a PC connected through the internet. Essentially, the idea of e-registration is to lead students to a convenient way of registering online. Students will be able to save their time, money, plus submit their information with just in few minutes. In additional, it can be done anytime, anywhere according to their preference, provided it is within the stipulated time period.

It is in this regard that this project looks at the student’s registration system at Imo State Polytechnic Umuagwo in order to design and develop an e-registration system for the school.

1.2 Statement of the Problem

From the background of the study, one can observe the following problems which prompted this project;

1. Difficulty faced by students in retrieving their lost receipt from bursary.
2. Inconveniences faced by students queuing to pay school fees and collect registration form.
3. Wear and tear that occurs during retrieval and manual handling of files, sometimes data get lost as a result.
4. Increase of paper work in the bursary department and course form registration center.
5. Difficulty experienced in updating of record in a file.
6. Misplacement, loss or damage of student’s record.
7. Inability of students to remotely register and access documents like school fees receipt.
8. Difficulty in locating registration at crucial times.

1.3 Objectives of the Study

The major objective of this project will be concentrated towards the development of software that will help in removing the problems encountered with student’s manual method of registration. That is to say, the general objective of the study is to develop e-registration software.

The specific objectives include;

1. To collect the detail record of students.
2. To create a database for the students.
3. To create an online transaction processing system for the payment of fees by students and generation of receipts.
4. To create an easy to use friendly user interface.

1.4 Scope of Study

This study focuses on the development of e-registration system for Imo state polytechnic Umuagwo. It shall include programs which will contain detailed information of the students since first date of enrollment and up to the graduating day including all students’ information and procedures required by the students during registration.

1.5 Significance of the Study

This project work “the design and implementation of an e-registration system will be of great significance to tertiary institutions in the sense that it will help in overcoming the problems of manual operations. Such problems includes; difficulty experienced in updating a record in a file, difficulty faced by students in retrieving their lost receipt from bursary, and inability of students to remotely register and access documents like school fees receipt.

This institution will make use of the software to access their student’s record. The institution will through the knowledge gained in this work discover the need to fully adopt this new system. The students also will greatly benefit from this project as it will enable them to have a new experience of registration when the system is finally adopted.it will also make them to embrace any policy strategy and innovational steps taken by the institution to enhance the quality of education in school.

 

 

1.6 Limitations of the Study

The act of carrying out a project work such as this was not an easy task. Several challenges were encountered by the researcher but efforts were made to ensure that they were overcome and that the objectives of the study were realized.

1. Unavailability of data and inadequate resource materials for researcher in this part of the country.
2. Time constraint was another issue the researcher has to battle with as a stipulated time was given for the accomplishment of this task.
3. The problem of financial constraint was also an issue of great concern. The meager income available to me had to be managed to realize this work.
4. The problem of interrupted power supply also affected my fastness in the design of my work.

In spite of these challenges the objectives of this study was realized as the researcher made judicious use of what was available.

 

CHAPTER TWO/Literature Review

2.1 Meaning of RegistrationDownload Full Material-N5000