Nepal was isolated from the western world during the period 1800 – 1950 AD and the industrial and scientific revolution during this period passed Nepal by. Initial interest in the field of biotechnology began after the establishment of Department of Medicinal Plants (Now Dept. of Plant Resources) and Royal Drug Research Laboratory (now National Medicine Laboratory (NML)) in early 1960s (UNESCO/RONAST, 2006). Nepal Academy of Science & Technology (NAST, then Royal Nepal Academy of Science & Technology (RoNAST)) and Nepal Agricultural Research Council (NARC) got established in 1980s which, in some sense, were the prime institutions conducting scientific research in Nepal. During late 1980s and 1990s, some organized efforts from Nepal Biotechnology Association (NBA) and Nepal Molecular Biology Society (NEMBIS) had been carried out to promote biotechnology though it was much limited within a handful of senior scientist.

But the true Nepali biotechnology revolution conflagrated after Kathmandu University (KU) launched a 4 year undergraduate program in biotechnology starting 2003. Since then 5 other institutions (Tribhuvan University, Whitehouse Institute of Science & Technology, Lord Buddha Education Foundation, SAAN International College and recently Kantipur Valley College) around Kathmandu have launched similar undergraduate and graduate programs in biotechnology. Few more groups were established during this period mainly Biotechnology Society of Nepal (BSN) that has been effective, to some extent, in uniting students, academia, government and industries and advocating biotechnology in Nepal.

Now, almost a decade has passed since the inception of Nepali biotech revolution but we have just started toddling. Developing biotechnology, which no doubt is a big-money science, in a resource-strapped (low technical infrastructure) country like Nepal is a huge challenge in front of us. However, I would like to focus on few of the critical challenges in Nepali Biotech that have been spoken yet unheard.

Applied vs Basic Science

As Prof. Mukunda Ranjit puts it, “Everyone (during 1960s to 90s) were after development and nobody wanted to do science” (Talk Biotech on Wednesdays – Episode 1). Indeed till date we have been applying knowledge rather than developing the knowledge itself. Although no written evidence is available, the entire Nepali science policies and strategies are based on promoting the application of knowledge/technology. This vision of applied science was much suitable back then but now we are in a dire need of inventing the knowledge so that we could sell it to others.

Just to give you an analogy, basic science is like manufacturing raw materials and applied science is like assembling and producing a final consumer product. Putting it in the other way, basic sciences forms the foundation upon which applied sciences rely just as the figure given below. But looking at the Nepali life-sciences sector, the foundation itself is very feeble and the current developments are overly mounted upon it. For example, there are lots of pharmaceutical and food industries in Nepal that has got well established for more than a decade. All these industries have been using the techniques and knowledge discovered abroad and is just functioning like an “assembly station” and hardly a handful of these industries are interested in R&D.

Developing basic science (or R&D) is like developing a culture which will certainly take a longer time but gives a solid foundation (like in North American and European countries) but if the we are to only strive for the applied science and never ever care about the basic science then there will come a time when the whole system will collapse (scenario well evident among South Asian countries). This is why around 40% of graduate degree holders (Masters and/or PhD) end up in a teaching job rather than doing research and inventing knowledge (Shrestha, 2012).

The field of Biotechnology has been victimized by the same scenario. There has been a trend in younger Nepali universities like Kathmandu University, Purbanchal University, Pokhara University and many other colleges to launch applied science based degree courses like biotech. No doubt the course has been designed consulting the national as well as international experts in the field. The overall courses of all the biotechnology degrees available in Nepal are much compatible with that of any North American or the European universities. But when most of the biotech students come to market after his/her graduation he/she will end-up jobless. What is the reason behind this? Most of the students complain that industries and the scientific community as a whole has not understood the role, responsibility and potential of biotechnology.  Almost all of the biotech graduates complain of being the jack of all and master of none!

The course has been designed mirroring North America and Europe where the basic science is well established and the scientific community there has well defined the role of biotechnology. But in the case of Nepal launching a biotechnology degree program was like jumping many strides ahead. And biotechnology program has been a lesson to be learnt for KU which otherwise had been overly successful in applied science based courses launched prior to biotechnology.

Well this had to happen in a country where the basic science is totally neglected. The scientific community has not understood the importance of biotechnology because the culture of basic science research is totally lacking in our country. Eventually this problem is growing bigger and bigger and if we are not to understand this aspect of science then we will not be able to keep up pace with the world in coming decades.

Having spent almost a year in Canadian universities and working across various labs here, my perspective towards biotechnology has changed totally. Biotech here is considered much like an industrial based, job oriented course rather than research oriented course. The term biotechnology is closely associated with industries and product development. However, the trend in Nepal is completely opposite!!

Brain Drain

It is needless to restate that we have been facing a serious brain drain and this is even more exaggerating among the biotech graduates in Nepal. But the most overwhelming thing is that Nepal ranks among the top 10 countries in the world to export international students at graduate level in the field of Science & Engineering to USA (Wasem, 2012). These data certainly indicate that despite being an under developed country, Nepal has been producing a lot of talented students and have been exporting in the global market in the field of science & technology. Provided a good environment certainly these talents can be utilized in the home country itself.

Till 2011, approximately 350 biotech graduates have been produced from various biotech colleges around Nepal among which 186 students have been graduated from KU alone. On an average every year around 120 biotech students are produced in Nepal itself. There are many more students studying biotechnology in India, Pakistan, Bangladesh, Europe, Australia and America adding up to the list.

A case-study (data as of May, 2012) carried out among the Biotechnology graduates (4 years B.Tech. program) from KU clearly indicates that there is an increasing trend of brain drain among biotech graduates. Majority of the students fly to European and North-American countries for their graduate studies. Strikingly, almost 98% of the biotech students graduating in 2007 had gone abroad (till 2012) for their higher studies (note: those students that have returned back to Nepal after completion of their graduate studies have also been categorized as students that have gone abroad). The subsequent batches of students seem to follow the same trend indicating growing frustration among the biotech graduates. This scenario is not very different when cases of biotech graduates from other colleges are considered.

Biotech Jobs??

Ironically, you will be surprised by the fact that almost every government institution dealing with biotechnology and/or molecular biology have a specialized “Biotechnology Division” and some recruited biotechnologist. But to our dismay, most of the people holding those posts are largely incompetent for the assigned job and are not much aware of the basics of biotechnology (as most of them are trained in other disciplines of life-science). I can vouch that even a fresh biotech graduate with limited experience knows much more (both theoretical as well as practical aspects) than the biotech job holders in government institutions, who have very limited exposure to “research”!!!!

Another taboo prevalent within our society is that certain institutions only prefer a “single breed” of graduates. For example, an organization working in agriculture will only accept a graduate in agriculture or forestry for a biotech position than a biotech graduate itself. This misconception must be wiped out from the roots.

But the major hurdle has been that the Public Service Commission (PSC) (Lok Sewa Aayog) of Nepal has not yet recognized biotechnology as separate discipline. At present a biotech graduate has to either register him/herself as a zoologist, botanist, micro-biologist to give PSC exams but a zoologist, botanist, micro-biologist will be eligible to hold biotech positions in government institutions. This is the bitter irony of Nepali biotech!!  Government has not been able to recruit competent biotechnologist and the competent biotech graduates are lying jobless and falling in line to fly abroad.

A Faint Spark of Brightness

Despite of all the problems laid out above, the recent moves by government has ignited renewed enthusiasm amongst the Nepali biotech community. The announcement made back in 2008 by the then Maoist lead government to shower US $125 million (12 fold increase) to science and technology development even managed to get published in the much prestigious Science magazine (Guo, 2008). Recently, Ministry of Science and Technology (MoST) has announced to establish National Biotechnology Center (NBC) by 2013. NBC aims to promote research and development in agriculture, health, environment and industry with an estimated cost of US $13 million over the course next five years (Science and Development Network). MoST has been enthusiastically facilitating for funding and foreign collaboration in various prioritized biotech based research projects. Another conference held recently in Kathmandu has revealed  some strategic plans for cooperation in the field of biotechnology between India and Nepal (Natural Prospects Of Biotechnology). Furthermore, few biotech ventures (from private funding) are adding up on the list every year which is a very good sign.

Source : http://blogs.nature.com/tradesecrets/files/2012/04/April_12-map.jpg

Something of Change

No doubt that Nepal is in a phase of socio-political transformation and lots of other issues have been prioritized rather than science and technology. A lot of biotech talents are migrating abroad due to the two decades of chaos in the country which is a serious issue. However, I receive this as an opportunity that Nepal can utilize in the coming decades. Looking back at our neighbor – China, majority of the credit for the booming Chinese Biotech goes the US-returned Chinese scientist who returned to their home land when China became more open to global business (Chinese Scientists Build Big Pharma Back Home). Nepal can create similar situation too. But the question still remains, is Nepal prepared (or is preparing) for this reverse-migration?

India’s biotech firms are largely focused on process innovations to improve affordability and accessibility of medicine among local and global populations whereas Chinese biotech firms are striving to create novel products in such areas as gene therapy and regenerative medicine (China’s biotech industry: An Asian dragon is growing). Being in the middle of the two, strategically very different, big power house of Biotech – China and India, Nepal certainly has a golden opportunity to tap the big biotech business. But for this we need more biotech entrepreneurs, more infrastructures and above all we need biotech engulfed within industries.

As Prof. Dayananda Bajracharya puts it “The public at large thinks science is too sophisticated for a country like Nepal,” (Guo, 2008) we need to take a holistic approach to develop the overall situation we are facing today. Nepal is beginning to realize that the way ahead is only possible through the path of Science and Technology (Kaphle et al., 2009). It may take another revolution to change things around – The Nepali-Biotech Revolution !!

Acknowledgements

I would like to thank Mr. Pawan Bashyal, Mr. Prajwal Rajbhandari, Ms. Manisha Bista and Mr. Aagat Awasthi for helping me collect the data of the KU Biotech graduates.

Nepal, geographically, is between Tibet (China) and India. These neighbors represent two distinct ethnicity – the Mongols from Tibet and the Aryans from India. It is natural to think and of course an intelligent guess would be that Nepalese are mostly the hybrids of Mongols and Aryans. Yes, indeed this is the truth but still the question is who came to Nepal first – the Mongols or the Aryans?

At present, scientific community has widely accepted the recent African origin of modern humans 200,000 years ago better known as “Out of Africa” theory. However, controversies still exist whether the early human originated in Africa (single-origin hypothesis) or were originated at several locations including Africa (multiple-origin hypothesis) (Harpending and Eswaran, 2005; Lui et al., 2006). It is believed that the modern human left Africa 125,000 years ago and reached the present day Middle-East Asia from where they dispersed into three different directions (at different time-scales) – one lineage to the Europe, second lineage towards China and the third lineage into South Asia (India).

A map of early human migrations ( Source: http://en.wikipedia.org/wiki/File:Spreading_homo_sapiens.svg )

The northeast Indian passageway connecting the Indian subcontinent to East/Southeast Asia is thought to have been a major corridor for human migrations. Indeed, abundant East Eurasian mitochondrial DNA (mtDNA) lineages have already been detected in the northeast Indian populations raising the possibility that the East Eurasian influence could trace its origin back to the dispersal of Tibeto-Burman people who arrived at Nepal via northeast India (Cordaux et al., 2004; Reddy et al., 2007). Recently, by comparing the Y-chromosome lineages between the Nepalese and the Tibetan populations, Gayden et al. have proposed that the East Eurasian genetic components had been introduced into Nepal from Tibet directly (Gayden et al., 2007; Gayden et al., 2009). But still this raised a major question – did Tibetan cross the great Himalayas to enter Nepal?

A recent study by Wang et al. entitled “Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes”, published in March 2012, finally came up with an answer.  For this, mtDNA was collected from 246 unrelated individuals from Kathmandu and Eastern Terai. Other data from both mtDNA as well as Y-chromosome was obtained from various published studies as detailed in Table-1 in the paper.

Sampling locations of the populations analyzed in this study. The Nepalese populations collected in this study are highlighted with solid pentacles, and the black dots represent the populations retrieved from the literature.

The northeast Indian passageway connecting the Indian subcontinent to East/Southeast Asia is thought to have been a major corridor for human migrations. Indeed, abundant East Eurasian mitochondrial DNA (mtDNA) lineages have already been detected in the northeast Indian populations raising the possibility that the East Eurasian influence could trace its origin back to the dispersal of Tibeto-Burman people who arrived at Nepal via northeast India (Cordaux et al., 2004; Reddy et al., 2007). Recently, by comparing the Y-chromosome lineages between the Nepalese and the Tibetan populations, Gayden et al. have proposed that the East Eurasian genetic components had been introduced into Nepal from Tibet directly (Gayden et al., 2007; Gayden et al., 2009). But still this raised a major question – did Tibetan cross the great Himalayas to enter Nepal?

A recent study by Wang et al. entitled “Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes”, published in March 2012, finally came up with an answer.  For this, mtDNA was collected from 246 unrelated individuals from Kathmandu and Eastern Terai. Other data from both mtDNA as well as Y-chromosome was obtained from various published studies as detailed in Table-1 in the paper.

Different loci of mtDNA and Y-chromosome are used as genetic markers to trace the great human migration and ancestry. The mtDNA traces the maternal lineage (as mitochondria of a zygote is always contributed by the mother) and Y-chromosome of course traces the paternal lineage (as only the father contributes Y-chromosome to a zygote destined to become a male). Often Mitochondrial Eve and Y-chromosomal Adam are referred to as the ancestors of every human being living on earth today. They are certainly not the first female and male on the earth as the Bible interprets, there were many humans in addition to Mitochondrial Eve and Y-chromosomal Adam, but they are the only surviving genetic markers/lineage till date that has been passed on to the existing human population. (For more information on the topic)

The study revealed that genetic components of East Eurasian (36.59%) and South Asian (51.63%) ancestry have comprised the vast majority of the Nepalese gene pool. Majority of the samples belonged to the already defined haplogroups, such as, M3, M5, M18, M30, M35, M43, D4, R8 and M60. (Haplogroup represents the group of individuals having similar alleles or SNP profile). Furthermore the study revealed a novel haplogroup characterized by variations 9266 and 11827, which was named as M81.

The Principal Component Analysis (PCA) of 43 populations under study revealed 3 among 5 of the Nepalese population clustered with Tibetan population. This means that 3 of the Nepalese population are very similar to the clustered Tibetan population.

[PCA is a very popular statistical technique to analyze High-Dimensional Dataset. Simply putting it, whenever there are multiple variables/factors describing a population then the dimension of data (or degree of freedom) is proportional to the number of variables which makes it very difficult to analyze as well as visualize the data. PCA reduces all these n-variables to 2 Components (or sometimes 3 if needed) so that it will make us easy to find correlation among the different variables. (For more information on the topic)]

Principle component analysis (PCA) of the populations under study.

The pairwise-distance data reveals that the Nepalese population is closely related to the Tibetan population. Following is a UPGMA tree constructed from the distance data in Table-2.

UPGMA tree constructed from the distance data in Table-2

The results of the admixture estimation analysis revealed that the Tibetans made major contribution to virtually all Nepalese populations (except for the eastern Tharu population)

Admixture analysis of the Nepalese by comparing with its potential parental populations (Tharu_E : Eastern Tharu) (Note: the error bars have not been plotted for the sake of simplicity)

On the basis of the constructed median networks, several features could be observed:

1. the Nepalese share some basal or internal haplotypes with the Tibetans;
2. the Nepalese harbor a number of unique haplotypes at the terminal level, most of which branched off directly from the nodes occupied almost exclusively by the Tibetan lineages and
3. only a few haplotypes are shared sporadically between the Nepalese and the northern Indians.

Taken together, the Nepalese lineages of East Eurasian ancestry generally show much closer affinity with the ones from Tibet, albeit a few mtDNA haplotypes, likely resulted from recent gene flow, were shared between the Nepalese and northern (including northeast) Indians.

[Note: Median Network is more or less similar to a phylogenetic tree but based on graph theory. These median networks are more informative than regular phylogenetic tree as the former considers the different evolutionary rate prevalent at different nodes of the network. Computationally it is termed as “Speedy Construction and Greedy Reduction” !!]

Median networks of haplogroups A11, C, F1c and Z.

Median networks of haplogroups G2a2 and M9a1a2a

Time estimation results revealed that haplogroups G2a2 and M9a1a2a have very similar ages ~6 kya (6,000 years ago). The previous work has suggested that the maternal genetic components from the northern East Eurasian was introduced into Tibet around 8.2 kya (Zhao et al., 2009) and time estimation resulted from this study fit the dating frame very well. Now it is convincing that the East Eurasian had entered Nepal across the Himalayas around 6 kya, a scenario in good agreement with the previous findings from linguistics and archeology. Yes, the Tibetans (Mongols) did cross the great Himalayas to enter Nepal even before the Aryans arrived.

Reference:

Wang HW, Li YC, Sun F, Zhao M, Mitra B, Chaudhuri TK, Regmi P, Wu SF, Kong QP, Zhang YP. Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes. J Hum Genet. 2012 Apr;57(4):228-34 (Download Full Text Article)

Related Papers:

1. Gayden et al. The Himalayas as a directional barrier to gene flow. Am. J. Hum. Genet. 80, 884–894 (2007).
2. Fornarino et al. Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol. Biol. 9, 154 (2009).
3. Su et al. Y chromosome haplotypes reveal prehistorical migrations to the Himalayas. Hum. Genet. 107, 582–590 (2000).
4. Cordaux et al. The Northeast Indian passageway: a barrier or corridor for human migrations? Mol. Biol. Evol. 21, 1525–1533 (2004).

Reblogged from Pairach Piboonrungroj:

The following article was published recently (23 March 2012) in the Science magazine – “Science in Nepal Needs Neighborly Aid” by Uttam Babu Shrestha highlighting this issue.

Compared with its neighbors, Nepal remains sluggish in economic development as well as investments in research and development [(1) and “Report notes China's influence in emerging Asian science zone,” News & Analysis, J. Mervis, 20 January, p. 274)]. While China and India have made substantial progress in science and technology, Nepal, sandwiched between the two countries, lags in basic science and technology infrastructure, high-quality education, retention of talented researchers, and qualified manpower.

China and India support Nepal’s development primarily by providing physical infrastructure. However, military assistance has overshadowed other aid. China has promised to provide military aid of US$7.7 million and to establish a military academy in Nepal. Likewise, India has resumed military assistance and promised to provide more military supplies in the future (2). In contrast, support is dismal for Nepal’s higher education, science and technology, and research and development. Furthermore, scientific cooperation between Nepal and its large neighbors is negligible (3)

Instability, corruption, and lack of technological development, as well as frequent disasters, have undermined economic development in Nepal. Because of the lack of research and development investments, about 40% of Nepalese who have master’s and Ph.D. degrees are teaching instead of conducting their own research (4). Thousands of talented Nepalese emigrated during the conflict and are now reluctant to return home because of limited opportunities.

After a decade-long conflict, Nepal is undergoing peace and a state-restructuring process. Rather than competing to provide military assistance to a country heading toward peace, China and India should foster innovation and economic prosperity by supporting Nepalese science and technology and research and development. An impoverished and uneducated Nepal is a greater threat to its neighbors than a Nepal that is enriched and educated.

It was not until 1953, when Watson and Crick cracked the model of Deoxyribonucleic Acid (DNA), the entire world turned their head towards the mysterious realm of biology. Watson and Crick explained how the heredity material, DNA, is passed on from the parents to the offspring and how DNA was able carry the information for all the life processes in a living organism. This concept of Central Dogma transformed biology from a descriptive science to a “happening” science. However, without the aid of the progress made in physical, chemical and mathematical sciences humans could have never achieved this.

In fact, it was the human skill to combine different approaches to solve a puzzle led us from the era of scientific discovery to the era of scientific mastery. Genomics and Bioinformatics are the two closely related disciplines that helped us in our journey to understand the life among and around us. Early works in the field of bioinformatics dates back to late 1960s but even till the early 1990s experts working in this field were known as “computational molecular biologist” (Bioinformaticist Vs Bioinformatician). One of the early bioinformaticians and a renowned figure in the field, Lincoln Stein, once announced in a conference that bioinformatics would cease to exist as a separate discipline ten years down the line (i.e. within 2012). But he later regretted in his own statement and asserted that bioinformatics isn’t disappearing but its stronger than before and will get even more stronger in the future (Stein, 2008).

No doubt, that majority of the science news in the late 20^th century until now has been mostly dominated by the genome sciences. However it’s not just the “pure” biologist that’s driving this field but new breeds of biologist are sprouting each with some distinct skills than the other. For example: Dr. Jim Kent who initially used to write programs for computer games eventually helped solve the biggest computational hurdle of the Human Genome Project. (There is another interesting article quite relevant to the topic “How Perl Saved the Human Genome Project”).

Following are the three breeds of experts visible in the field of genome science and bioinformatics (nevertheless all these three breeds of experts have subtle difference in terms of their area of work).

1. Genomicist: These are the biologist who are more focused in “-omics” studies. Genomicist like to divide their time between the wet and dry labs. They are more concerned with high-throughput analysis and has fairly good skills in bioinformatics.
2. Bioinformatician: Generally a bioinformatician has a strong background in molecular biology and genomics and also good skills in mathematics, statistics and computer sciences. They are mostly interested in high-throughput data analysis and exploit bioinformatics tools to solve key biological problems.
3. Computational Biologist: These experts have a very strong background in mathematics, statistics and computer science but a fairly good background in biology. They are mostly involved in algorithm design and development of various bioinformatics tools.

The scientific landscape is gradually changing from a hypothesis-driven science to a data-driven science. Since the introduction of the 454 Pyrosequencing technology in 2005, which marked the beginning of the Next Generation Sequencing (NGS) era, bioinformaticians have been inundated with sequencing data. Just a few days back, on February 17, 2012, a ground breaking sequencing technology by Oxford Nanopore was announced in the Advances in Genome Biology and Technology (AGBT) conference. It was a big buzz all over the popular social media and that morning everyone in our department was talking about it. A miniaturized sequencing device called MinION, which is just like a USB flash drive in terms of size and shape, will just put the cost of sequencing to $900. This breakthrough can put genome sequencing right to the doctor’s table within the beginning of next year and revolutionize the way we deliver health-care. But on the other hand, it will further sky-rocket the sequence data volume into an unimaginable height (Blogs on MinION: Pathogens: Genes and Genomes; genomes unzipped).

The bottleneck is however not the sequencing technology but various computational challenges like data analysis, visualization, integration and above all, the skills of the bioinformaticians have become a rate limiting step (Green ED et. al., Nature 2011). Bioinformaticians are still struggling with how to interpret the huge chunks of data. Furthermore there are several hardware challenges too.  Accessing and analyzing huge datasets requires large amounts of data to be frequently transported over a ‘cluster’, ‘grid’ or even a ‘Cloud’. One of the noted challenges is readily visible in the world’s largest genome sequencing center – Beijing Genome Institute (BGI). BGI has been using computer disk to transmit the sequence data to its collaborators mailing via a courier like FedEx. If transmitted using internet the voluminous data could take weeks to be transferred (DNA Sequencing Caught in Deluge of Data).

As portrayed in the famous novel by Alexandre Dumas – The Three Musketeers, the three friends Athos, Porthos, and Aramis live by the motto “all for one, one for all” (“tous pour un, un pour tous“). Similarly, the three musketeers of the genome sciences – Genomicist, Bioinformatician and Computational Biologist all work for a same cause with different set of skills which is vital to solve the major problems outlined above.

Capriotti E, Nehrt NL, Kann MG, Bromberg Y. Bioinformatics for personal genome interpretation.Brief Bioinform. 2012 Jan 13.

Abstract:

An international consortium released the first draft sequence of the human genome 10 years ago. Although the analysis of this data has suggested the genetic underpinnings of many diseases, we have not yet been able to fully quantify the relationship between genotype and phenotype. Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. Many resources aim to identify and annotate the specific genes responsible for the observed phenotypes. Some of these use intra-species genetic variability as a means for better understanding this relationship. In addition, several online resources are now dedicated to collecting single nucleotide variants and other types of variants, and annotating their functional effects and associations with phenotypic traits. This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants. In this work, we review the most important developments in the field-the databases and bioinformatics tools that will be of utmost importance in our concerted effort to interpret the human variome.

Click here for the full text article

This script uses a BioPerl module “Bio::DB::GenBank“. All the accession number must be present within the file accnumber.txt each separated my a comma. And also, file accnumber.txt must be present within the same directory as that of the perl-script. After successful execution it will generate a file sequence_dwnl.fa containing the sequence in fasta format.

#!usr/bin/perl -w

use strict;
use warnings;

use Bio::DB::GenBank;

open (INPUT_FILE, 'accnumber.txt');
open (OUTPUT_FILE, 'sequence_dwnl.fa');

while()
{
	chomp;
	my $line = $_;
	my @acc_no = split(",", $line);
	my $counter = 0;

	while ($acc_no[$counter])
	{
		$acc_no[$counter] =~ s/\s//g;

		if ($acc_no[$counter] =~ /^$/)
		{
			exit;
		}

		my $db_obj = Bio::DB::GenBank->new;
		my $seq_obj = $db_obj->get_Seq_by_acc($acc_no[$counter]);
		my $sequence1 = $seq_obj->seq;

		print OUTPUT_FILE ">"."$acc_no[$counter]","\n";
		print OUTPUT_FILE $sequence1,"\n";
		print "Sequence Downloaded:", "\t", $acc_no[$counter], "\n";

		$counter++;
	}
}

close OUTPUT_FILE;
close INPUT_FILE;

exit;

It was presented in the recent “Fourth International Barcode of Life Conference” held at The University of  Adelaide, Australia from 28 Nov – 3 Dec 2011. The presentation also includes narration from the author.

It was presented in the recent “Fourth International Barcode of Life Conference” held at The University of  Adelaide, Australia from 28 Nov – 3 Dec 2011. The presentation also includes narration from the author.