Genomics
The basic concepts of genome assembly
Genome, as we all know, is a complete set of DNA in an organism including all of its genes. It consists of all the heritable information and also some regions which are not even expressed. Almost 98 % of human genome has been sequenced by the Human Genome Project, only 1 to 2 % has been understood. Still the human genome has to be discovered more whether it would be in terms of genes or proteins. Many sequencing strategies and algorithms have been proposed for genome assembly. Here I want to discuss the basic strategy involved in genome assembly, which sounds quite difficult but is not really complex if understood well.
Basic strategy involved behind discovering the new information of genome is explained in following steps:
- First of all, the whole genome of an organism is sequenced which results in thousands or hundreds of different unknown fragments starting from anywhere and ending upto anywhere.
- Now, since we don’t know what the sequence is and which fragment should be kept near to which one, the concept for ‘Contigs’ is employed. Contigs are the repeated overlapping reads which are formed when the broken fragments comes to each other only by matching the overlapping regions of the sequence. It means that many fragments which are consecutive are joined to form contig. Many such contigs are formed during the joining process.
- Now, the question that arises is how come we know that a fragment which may be a repeat has been kept in its right place as a genome may have many repeated regions? To overcome this, paired ends are used. Paired ends are the two ends of the same sequence fragments which are linked together, so that if one of the end of the fragment is aligned in lets say contig1 then the other end which is a part of the former will also be aligned in the same Contig as it is the consecutive part of the sequence. There are various software with the help of which we can define different lengths of the paired ends.
- After that all the Contigs combine to form a scaffold, sometimes called as Metacontigs or Supercontigs, which are then further processed and the genome is sequenced.
All of this is done by different assembly algorithms, mostly used are Velvet and the latest is SPADES.
According to my experiences, more efficient algorithms are which may provide us large information in one go. Just imagine that we got a thread of sequence with unknown base pairs, then what would we do with that thread and how would we identify and extract the useful information from this thread??
Thank you for reading, Don’t forget to share this article if you like it.
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genozip is a tool for lossless compression of large files including VCF, FASTQ, and SAM/BAM files [1]. In this article, we explain the usage of the genozip tool for the compression and decompression of these files. (more…)
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Bioinformatics News
Mycobacteriophages and their potential as source against Mycobacterial active biomolecules
So, today is the great festival of Christmas……! Birthday of The Son of God.. And on this Auspicious day, We want to present before you all the power of Nature… How nature itself provides solution against the problem raised within it….. We all are aware of the epidemics of threat created by Mycobaterium tuberculosis and other related species. But, down here in this article we show how nature provides the solution against it.
As we know Bacteriophage (Bacterio= Bacteria’s, Phage= eater) infects several bacterium species. In contrast to it, a Mycobacteriophage is a member of a group of bacteriophages that infect mycobacterial species as their hosts e.g., Mycobacterium smegmatis and Mycobacterium tuberculosis, the causative agent of tuberculosis.
The rising incidence of tuberculosis, emergence of multi drug resistance in Mycobacterium tuberculosis and a slow progress in finding new drugs makes mycobacteriophage a potential candidate for its use as a diagnostic and therapeutic tool against TB.
All the characterized Mycobacteriophages are double-stranded DNA (dsDNA) tailed phages belonging to the order Caudovirales. Most are of the family Siphoviridae , characterized by long flexible non contractile tails, whereas phages of the family Myoviridae, have contractile tails. There is a notable absence of mycobacteriophages from the family Podoviridae (containing short stubby tails), arising the question whether long tails are needed to traverse the relatively thick mycobacterial cell envelope. dsDNA tailed phages are either temperate, forming stable lysogens with a turbid plaque or lytic, forming clear plaques in which the host cells are killed. Mycobacteriophages can also be studied by the morphology of the plaques which vary in size and shape. Plaque morphology also depends on the burst size, which is the number of phage particles released on the lysis of the infected bacteria.
Genometrics of 70 sequenced Mycobacteriophages
Since the mycobacterial cell wall consists of a mycolic acid rich Mycobacterial outer membrane, attached to an arabinogalactan layer that is in turn linked to the peptidoglycan, it poses significant challenge to the phages. This challenge is met by a set of proteins, namely Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, holins that regulate lysis timing, and the endolysins (LysinAs) that hydrolyze peptidoglycan.
Phages affect hosts with a holin-endolysin system essential for programmed lysis. Endolysin is found to be associated with a protein component of the phage tail involved in facilitating the penetration of the murein during injection of the genome into the host. Holins are small membrane proteins that form holes in the membrane through which the endolysin can pass. Holins control the length of the infective cycle for lytic phages so as to achieve lysis at an optimal time.
Endolysins can be a source of potential antibacterial because of its specificity (targeting only a few strains of bacteria) and thus replacing antibiotics (which have a more wide ranging effect), their low probababilty of developing resistance in Mycobacterium and novel mode of action.
Bioinformatics can assist this particular field of research by finding several other proteins existing on this planet or to prepare other such options having similar pharmacophore (physical and chemical attributes) properties. We can demolish the various disease threats by using natural options provided to us and can remain healthy on this planet. The only point to be remembered for this is,
NATURE CAN SATISFY OUR NEEDS, BUT IT CANNOT SUSTAIN OUR GREED….. AS A HEALTHY BODY CONSISTS OF A HEALTHY MIND, THE SAME WAY.. A CONSERVED PLANET CONSERVES ITS SPECIES TOO…..
(A major part of this article consist of some texts copied from
Hatfull, Graham F. “Mycobacteriophages: genes and genomes.” Annual review of microbiology 64 (2010): 331-356.
for any other information related references and queries, please let us know at [email protected]
The Microbial Pan Genome is the union of genes shared by genomes of interest. This term was first used by Medini in 2005.
As the needs say the importance of sequencing of genomes, it is equally important to visualize them. There exists some tools to visualize the genomes,but they are static and standalone, (more…)
Fozail
October 17, 2015 at 5:31 am
I am delighted to read your article about basics of Genome assembly. But I would like to add on some fact over the same as well. You simply drafted out the steps involved in the GA and what methods are being used.
Apart from what you have mentioned in your article, there exist a number of algorithms/methods being used for Genome assembly. These are
1. SSAKE
2. SHARCGS
3. VCAKE
4. Newbler
5. Celera Assembler
6. Euler
7. Velvet
8. ABySS
9. AllPaths
10.SOAPdenovo.
These have been proved much better than other existing versions of Genome assembler, based on K mer and de Bruijn Graph theorem.
You can read a full text article whose link is provided here, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646.
Basically, using the above algorithms two ends of similar thread are overlapped in hierarchical manner and then grouped into contigs and contigs into scaffold, sometimes called as metacontigs or supercontigs. ANd them they are further processed into different format of reads.
Muniba Faiza
October 17, 2015 at 4:34 pm
Yes you are right sir, I forgot to mention the scaffold step because I wanted to give the overview of the genome assembly, and that’s why i didn’t mention much about the algorithms except the latest one, i.e., Spades. But I will mention the scaffold step in it.
Thank You
Fozail
October 17, 2015 at 5:08 pm
You are most welcome..