Coronavirus Genomics and Bioinformatics Analysis

Basic information about coronavirus:

Coronaviruses are a family of viruses that can cause illnesses such as the common cold, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). In 2019, a new coronavirus was identified as the cause of a disease outbreak that originated in China.

Figure:CoronaVirus

The virus is now known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease it causes is called coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic.

Human Coronavirus Types

Coronaviruses are named for the crown-like spikes on their surface. There are four main sub-groupings of coronaviruses, known as alpha, beta, gamma, and delta.

Human coronaviruses were first identified in the mid-1960s. The seven coronaviruses that can infect people are:

Common human coronaviruses

1. 229E (alpha coronavirus)
2. NL63 (alpha coronavirus)
3. OC43 (beta coronavirus)
4. HKU1 (beta coronavirus)

Other human coronaviruses

5. MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS)
6. SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS)
7. SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19)

 Symptoms

Signs and symptoms of coronavirus disease 2019 (COVID-19) may appear two to 14 days after exposure. This time after exposure and before having symptoms is called the incubation period. Common signs and symptoms can include:

• Fever
• Cough
• Shortness of breath or difficulty breathing

Other symptoms can include:

• Tiredness
• Aches
• Chills
• Sore throat
• Loss of smell
• Loss of taste
• Headache
• Diarrhea
• Severe vomiting 

Bioinformatics Analysis:

The drastic increase in the number of coronaviruses discovered and coronavirus

genomes being sequenced have given us an unprecedented opportunity to perform genomics

and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest

genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from

32% to 43%. Variable numbers of small ORFs are present between the various conserved

genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera,

Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002,

with estimated substitution rate of 410-4 to 210-2 substitutions per site per year.

Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, betweenMHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.[for more information about this research paper:https://www.mdpi.com/1999-4915/2/8/1804]

Information Technology Works

What is Information Technology?

Well it is simple. Information technology (IT) involves the study and application of computers and any type of telecommunications that store, retrieve, and send information. IT involves a combination of hardware and software that is used to perform the essential tasks that people need and use everyday. 

Most IT professionals will work with an organization and technically understand what they need in order to meet their needs, showing them what the current technology is that is available to perform their required tasks, then their current Implementing technology in the setup, or creating an entire new set up.

Who are IT professionals, and what do they do?

Some IT people work behind the scenes to ensure that all the information systems we offer can run smoothly. These are database, network and system administrators.

• Others help in designing these information systems according to the needs of the organization. These are database, network, and system analysts.
• Others help develop hardware and software to make these systems more robust, reliable, and secure. They are hardware and software engineers.
• Still others ensure that this information is presented to users in a clear, useful, dynamic manner. These are web developers and designers.
• Instead of tran IT professionals, we will tackle the broader subject of IT by looking at undergraduate, graduate and professional certificate programs.

 Then we'll look at the most popular IT job title in detail, explaining what that person does and how they do it. We will look at salary expectations and overall job outlook for IT careers.

1) Undergraduate IT Program

Undergraduate IT degree programs and majors can be divided into three general categories: information science, computer science, and engineering. However, it should be noted that each of these majorities overlaps significantly with each other, with some courses called computer science in one school and engineering in another.

Information science, alternatively called information technology, is one of the broadest and most IT majors. Information science majors start from the beginning, learning common programming languages ​​and mathematical algorithms that make up hardware and software. They will then learn about operating systems, databases, networks, and security. Once they understand how this basic system works, they learn how to analyze the needs of an organization or business to create the best and most secure information system.

2) Graduate IT Program

Graduate school is a time to focus your education on a particular field of study and to understand and explore it deeply. For students interested in graduate level IT programs, the variety of programs available is as diverse as the IT profession.If you do a master's degree or doctorate in information technology, computer science or computer engineering, you will see that many of these courses are found at title graduate level. The main difference between undergraduate and graduate programs in these areas is the depth of coursework and the depth of original research opportunities.

For example, students in the university's graduate program in electrical and computer engineering take courses similar to the graduate program, but at a higher level, such as:

• Advanced Digital Integrated Circuit Design
• Advanced computer architecture
• The art and science of system level design
• Special Topics in Communication: Network Management and Control

Since graduate school has a time to ease your studies, several graduate IT programs have also been designed to develop specific job-related skills. For example, students who oversee the job of network and system analysts or administrators may obtain a master's degree in Information Networking (MSIN) or Information Security Technology and Management (MSISTM).

                                                                                              -Shweta Adsule.

Important Algorithms for Database Searching ·

Important Algorithms

• Needleman and Wunsch (1970)

A global alignment that was first developed without gap functionality: The method uses a dynamic procedure, which is more efficient and faster in comparison with the calculation of all possible alignments. This calculation is still too time-consuming for the analysis of huge databases. It is very time intensive due to its dynamic procedure. A dynamic procedure is a solution to a problem that is broken down into subproblems, and the best results are then compared.

• Smith and Waterman (1981)

A local alignment that was originally developed without gap functionality: The method is very similar to that of Needleman and Wunsch and also quite time-consuming.

• FastA (Pearson and Lipman 1988)

A local alignment that is very fast due to the use of a heuristic method (making assessments to get almost exact results): The method identifies short word regions and then uses a dynamic procedure to obtain a gapped alignment.

• BLAST (Altschul et al. 1990)

A local alignment that can identify segment pairs of fixed length quickly due to the use of a heuristic method. Segments are then prolonged until preset threshold parameters are reached. BLAST is up to 100-fold faster than the Smith and Waterman algorithm.

• Gapped BLAST (Altschul et al. 1997)

A local alignment that looks only for a single segment pair: This segment pair is then prolonged by gaps in both directions. The gapped BLAST algorithm is three times faster than the ungapped BLAST algorithm.

WHAT IS ALIGNMENT?

Alignment

“It is the comparison of  two or more DNA or protein sequence by searching for a series of individual character or character pattern.”

1) Pairwise sequence alignment:-

          a)Local Alignment:-

·       The alignment stop at the end of region of strong similarly and much high similarity is given to finding this local region.

·       It consider only match region.

·       Dashes in the sequence indicate sequence is not included in the alignment.

·       Vertical bar indicate identical region in the sequence.

·       Highest matching called seed.

·       Smith waterman Algorithm is used in this alignment.

e.g. BLAST(Basic local Alignment search tool.)

a)   Global Alignment:-

·       In a global alignment attempt is made to align the entire sequence using all sequence character upto both ends of each sequence.

·       It is consider match, mismatch and gap region also.

·       Sequence that are quite similar and approximately the same length are  suitable candidate is for global alignment.

·       Needleman wunsch Algorithm is used in this alignment.

e.g.FASTA

Principle method for pairwise sequence alignment:-

                                       a) Dot Matrix

                                        b) Dynamic Programming algorithm

a)   Dot Matrix:

This method displays any possible sequence alignment as diagonal on the matrix.Dot matrix analysis can readily reveal the presence of interaction, Deletion and direct and indirect repeat that are more difficult to find out by the other method .This method was first described by Gibbs and McIntyre (1970).

Features of Dot matrix:

The Dot matrix should be visible on Computer terminal thus providing an interactive environment so that different types of analysis.

Use of colour dots can enhances the detection of region of similarity.

Methods of Dot Matrix:-

1)In a Dot Matrix method for sequence comparison one sequence A is listed across the top of the page and the other sequence B is listed down the side.

2) Starting with the first character B the comparison then move across the page in the first raw and places a dot in any column ,where the character in A is the same.

3) The second character in B is then compared to the entire A sequence and the dot is placed in row two wherever the match occurs.

4)This process is continued until the page is filled with dots representing all the possible matches of A character with B character.

5)Detection of matching region may be include by filtering out random matches in the Dot matrix.

6)A large window size is generally used for DNA sequence than for protein sequence, because of the number of random matches expected between unrelated sequence is much greater due to the  use of only 4 DNA symbol as compared to 20amino acid symbols.

                    Sequence A: AGCTAGGA

                    Sequence B: CACTAGGC

7) To maximize the number of matches the resulting alignment could be:-

                          —AGCTAGGA—

                           CA—CTAGG—C

   b) Dynamic Programming algorithm:-

   1)It is a method of sequence alignment ,that can take gaps into account but required a manageable number of comparison.

2)DNA is an efficient recursive method to search thought all the possible alignment and find the one with an optimal score.

3)DNA usually consists of the following three component .

               i)Recursion relation

              ii)Tabular computation                     

              iii)Traceback

4)Needleman and Wunsch first introduced a dynamic programming algorithm for comparing two sequence in 1970.

                                                                                                                  

                                                                                                                       --Shweta Adsule

Important Database

Bioinformatics:

“It is a computational approach with IT technology used to solve the problem of life sciences”.

                 Father and mother of bioinformatics “Dr.Margarat Okley Dayhoff”.

     Indian father of bioinformatics “Dr.G.N. Ramachandran”.

          Types of Biological database:-

a)    Primary database:-

·  It is basic type of database.

· Information is direct submission.

· It is Low annotated database.

(Annotation:- It is attachment of biological  information to newly discovered sequences.)

                   b) Secondary database:-

·       It is Derived type of database.

·       The information derived from primary submission .

·       It is highly annotated database.

                     c)Composite database:-

        ·       It is mixture of primary and secondary database.

                   Database:-

 NCBI(National Center for Biotechnology Information):-

URL:-(http://www.ncbi.nih.gov/Entrez/)

1)   It is division of the National Library of Medicine (NLM) at the National Institutes of Health (NLM),a federal agency of the US government.

2) The Entrez site for PubMed,Nucleotide,genome, protein and structure database is being maintained in the USA.

3) The mission of the NCBI is to ensure that the growing body of information from molecular biology and genome research is placed in the public  domain and is accessible freely to all facets to all the scientific community in ways that promote scientific progress.

                        EBI(European Bioinformatics Institutes)

                     URL:-http://www.ebi.ac.uk/)

1)     It is poorly working in the field of bioinformatics.

2)     It is a center for research and services in the field of bioinformatics.

3)    It is a non-profit academic organization in hinxton, Cambridge, UK.

4)  It is a site for nucleotide and protein sequence, protein structure and signature, seqs(SRS),and literature database.

5)    The institute manages database of biological data including nucleic acids, protein sequences and macromolecular structures.

6) EBI is large public institutes funded by the UK government.

                        SIB(Swiss institutes of bioinformatics)

                     URL:-http://www.isb.sib.ch

                      1)The Switzerland Institute of bioinformatics(SIB)  is an qusi- academic,

                        non-profit foundation whose mission is to promote research.

                    2)Development of databanks and computer technologies ,teaching and service  activities in the field of bioinformatics,both individually  with international                                collaborators.

      Nucleotide Sequence Database :-

               1)The International Nucleotide Sequence Database Collaboratio(INSD) consiste nucleotide  sequence database from three groups.

·       DNA  Databank of Japan(DDBJ) of National Institute of Genetics,Japan.

·   GenBank of National Center for Biotechnology Information(NCBI),USA.

· The European Molecular Biology Labs(EMBL)Data Library of European Bioinformatics Institute,UK.

2)Databases EMBL,GenBank and DDBJ are the primary nucleotide sequence database.

     

                  

Some important databases &Software in Bioinformatics.

 Databases:~

There are three major ones:

*Nucleic acid sequence database

• E.M.B.L. Nucleotide sequence database
• NCBI Gene bank






• D.D.B.J.

*Protein sequence database

• Swiss prot
• P.I.R.
• MIPS

*Protein structure database

• Protein database

Some important software

There are many software related to BioInformatics available on different Internet Servers. The major ones are: -

• Database search
• WAIS
• Sf gate
• Gate entry
• Pub mid
• Entrezz
• Homology search
• Blast
• Festa
• Smith-Waterman
• Sequence analysis
• DNA to AA
• Proscan
• Signal signal
• Sspn
• Gene Feature
• ORF Finder
• T.F. Search
• Motif
• The block
• M.E.E.E
• Clust alw
• Prediction of Secondary Structure
• Second structure
• Prediction predict protein

                                                          ~Shweta adsule.

Growing opportunities in the growing market of software development

If you are interested in your computer and technology, you can give a lot of name and price to IT companies like IBM, Intel, Microsoft and Google. As a software development engineer, you can quickly climb the stairs of success. This is the reason that the trend of youth in the study of computer science has increased rapidly nowadays. Due to the growing market of internet, websites and software applications, the demand for professionalism has increased in this area.

Work :-
The role of the developer in the software industry is very important. Software development engineers work on designing, developing application and application technology, or programming languages ​​like assembly, assembling and tool development. It is their responsibility to create new software according to the needs of client companies.They have to work on the demand and specification of the client constantly and deliver the timely delivery of the product. Along with the old software applications, they also have the task of updating them by working on new functions, specifications, weaknesses and speed. At the same time, they keep an eye on market needs. Since software development is a teamwork, they have to co-ordinate with the company's designers and content producers team. Programmers also have their own role in this field. But they mainly work on programming coding.


Skill:-

The demand of skilled people in the software industry is increasing steadily. Generally, companies are giving preference to those who have experienced four to five years of experience for software development jobs. Especially knowledge of languages ​​should be knowledge. In addition, understanding of Linux OS, Trouble Shooting and D-Bugging Skills, Data Structure and Algorithm are important. Such professionals are also expected to keep good communication skills and connoisseur eye.

Qualification:-

Students who wish to work in the field of software programming or development can do courses in programming, computer science or software engineering. For this, it is important to have a graduate with a science stream. Masters Degree in Software Engineering can also be done. Similarly you can get admission in this profession by getting BE, B-Tech, ME, MS or M-Tech degree.

Job Opportunities:-

If the job market trends are seen, the demand of software developers will continue in the coming years. Especially, the demand for professionals associated with the programming sector is expected to be very much in the country and abroad. According to the Bureau of Labor, by 2018, job prospects in the field of software engineering will increase by about 32 percent. Because of the demand of applications for internet and websites, there are also plenty of possibilities for programmers. You can find jobs in this field as Network Administrator, Database Administrator, Network Programmer, Tester, System Analyst, Business Analyst, System Engineer, Web Designer and Technical Support etc. At present, due to outsourcing in the IT sector this profession is full of great potential.

Salary:-

New-technology and software have made people's life convenient. Engineers who develop these softwares and technology also have good salaries. In many large companies, they get many opportunities like loans, insurance and reimportments, along with salaries and career growth. If you talk about the salary structure, professionals associated with this field get 25 to 40 thousand rupees per month in the initial period. After some years of experience, the salary can be in lakhs. This is the reason why this profession is one of the top high-paid salary jobs.

Main Institutes in India

- Indian Institute of Technology, Delhi

http://www.iitd.ac.in

- University of Chandigarh, Chandigarh

http://www.cuchd.in

- Roorkee College of Engineering, Uttarakhand


http://www.rceroorkee.in