Exploring the Ensembl Genome Database and its Applications

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The Ensembl genome database
Authors: T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V.
Curwen, T. Down R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk,
H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust,
E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A.
Ureta-Vidal, I. Vastrik, M. Clamp
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Contents
Introduction.................................................................................................................................................3
GENOME ANNOTATAION..................................................................................................................4
Ensembl Web Site...................................................................................................................................5
Software Design of Ensembl...................................................................................................................5
Annotation Pipeline of Ensembl..............................................................................................................6
Figure: Ensembl Pipeline System............................................................................................................6
DAS (Distributed Annotation System)....................................................................................................7
Contacting Ensembl.................................................................................................................................8
Conclusion...............................................................................................................................................9
References.............................................................................................................................................10
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Introduction:
The article selected for this brief is The Ensembl genome database. Genome sequencing provides
the shortcut through which scientists can detect genes efficiently. These sequences contain
information about the genes where they are located. In the initial time manual annotation of
genome sequences were not sufficient to the researchers to the access timely to latest data. This
project was developed to annotate the gene automatically and combine it with biological data so
that it can be available to public through the web. Range of the data is increasing day by data as
more genomes are added to the Ensembl project. This project provides the database for genome
annotation of humans. In this brief we will discuss about genome annotation, website, software
system and pipeline of Ensembl database.
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GENOME ANNOTATAION
Annotation of genes means to plot a gene into genomes. It is necessary to predict the genes.
Predicting the genes in eukaryotic organisms is not appropriate as it predicts incorrect structures
of genes. Genes are mapped in three steps. The first step is called as targeted stage in which
various analyses are run in the genomes which consist of masking and prediction of ab initio
genes. In next step novel genes are formed by aligning the proteins to the genomes. In last step
peptides are created by running the programs to the genomes. Now the exons from these peptides
are assembled and the genes are formed. By following the above steps transcripts are created.
Every transcript id consists of 11 digits no. Those transcripts which are starting from ENST are
human genes.
Ensembl is used to annotate EST (Expressed Sequence Tags) models and non coding RNA.
ESTs are used in identifying new isoforms. ESTs sequences have very high degree of error.
Various approaches are made to combine EST with Ensembl gene because they are useful in
predicting non coding exons. Algorithms used are exonerate and EST_ genome. Human genes
can also be determined through genome shotgun. (Hubbard et. al., 2002)
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Ensembl Web Site
This web site provides variety of genome information. Currently there are 9 species present in
Ensembl such as, mouse, human, zebra fish, rat, fruit fly, puffer fish and mosquito. There are >
twenty web pages which shows the different form in which data is present. It also provides
similarity searching through BLAST and SAHA. The website is constructed on an open-floor
which consists of Apache & MySQL. MySQL is the relational database which is very fast and
can process databases of 80GB or much more. The data which is displayed in the website arises
through the pipeline of Ensembl & it is fetched through API of PEARL. (Stalker, et. al., 2004)
Software Design of Ensembl
The software design of this project is very portable which means we can add or remove the
components when we want. The database used in this project is MySQL relational database.
Different languages are used in this project such as main code is written in Pearl language, some
other extensions are present in the C language & interfaces are present in Java. Pearl software is
inherited from the object design of biological developers by Bio Perl. The developers involved in
creating Ensembl database project have created reusable components of the software which also
describes the entities of biology like chromosomes, transcript, proteins and genes.
As MySQL is available free for all the developers which are noncommercial so any organization
has the right to install a copy of MySQL so that they can download the data of Ensembl from the
website. If there are less complex queries then SQL can easily handle them but for the complex
queries Perl Objects of Ensembl are used.
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Annotation Pipeline of Ensembl
The analysis of the Ensembl and the pipeline of the annotation are based on some sets of
heuristic rules. These predictions on the genes are depending on experimental evidence which
are imported manually by curated UniProt and partially curated NCBI. UTRs are also associated
with the records of EMBL mRNA. We cannot say with full guarantee that UTR sequences are
complete and there is also no surety that genomes of the Ensembl and the pipeline associated
with the Ensembl have clue so that we can predict full regions of the UTR. This pipeline is
annotated to the very little number of species and at present there are no such algorithms which
can provide good results on genomic scale.
Figure: Ensembl Pipeline System (Potter, et. al., 2004)
In this system a Rule Manager is present who submit the investigation of the job to the compute
farm by using LSF (Load Sharing Facility). Remote node is present in this pipeline system in
which job of the individual starts executing, then Runner Script is responsible for obtaining the
information of the job from the core and pipeline databases and it regenerate the object of job.
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By doing this RunnableDB is created and it is used to call the particular methods like run,
fetch_input, write_output, etc. so that the analysis can be run. (Potter, et. al., 2004)
DAS (Distributed Annotation System)
DAS stands for Distributed Annotation System. It is that blueprint of any protocol by which data
of genomic regions can be requested and can be returned. It stores the annotation sequences in
the distributed manner by using third party. It is used to circulate the data on the Internet so that
scalability of the system can be improved. The approach used in circulating the data on Internet
is based on divide and conquer method.
DAS can be used in following ways:
 Bio java servers of DAS are used for making the content available to the clients of third
party.
 If users doesn’t want to be configured with the clients of the other party to see the content
of genomes of human then Ensembl contigview is used to configure so that it behave as
client of Distributed Annotation System which means view is already configured through
the sources of Distributed Annotation System.
 There are many users who don’t want to set up any server then in DAS servers can be
uploaded with little amount of annotation.
DAS can be replaced in future by SOAP (Simple Object Access Protocol) which is used in
providing the protocols of lightweight so that the information can be exchanged in the distributed
and decentralized environment. The main drawback of this is that communities are not able to
develop their own annotations of DAS and they had to learn XML as well as software of Web to
develop the DAS servers. (Dowell, et. al., 2004)
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Contacting Ensembl
In order to expect a reply from Ensembl users need to write their email address. If users will send
queries without providing their contact details then will not be able to expect a reply from them.
Once a user is login into the web page of Ensembl then at the footer of that website an option
comes ‘Contact Us’. User can also resend their queries if they are not getting reply from them.
Ensembl is a project which is jointly made by two organizations EBI and Sanger Centre, present
in Cambridge, UK.
Users can subscribe to the [e-mail] to get announcements of any updates:
Users can also subscribe to the mail- [e-mail] for getting development of day to
day.
If users want to send any requests or need any support from them then they can send the mail to
[e-mail] which is the helpdesk. (TORIA, 2017)
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Conclusion
We have successfully created the report on the topic The Ensembl genome database and we have
covered all the essential points related to this topic. The infrastructure of this project is growing
day by day. All the genes of the Ensembl are depending upon the biological clues. Any one gene
of Ensembl can arise from mRNAs and proteins in many databases. Our priorities are looking
forward for the more species and to provide the essential services for the interpretation of the
genomes and to enhance the interface of the web.
This report includes introduction of the project, genome annotation of Ensembl, website of
ensembl, annotation pipeline and distributed annotation systems.
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References
Barker, D., Birney, E., Cameron, G., Clamp, M., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen,
V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Hubbard, T., Huminiecki, L.,
Kasprzyk, A., Lijnzaad, P., Lehvaslaiho, H., Melsopp, C., Mongin, E., Pettett, R., Pocock, M.,
Potter, S., Rust, A., Schmidt, E., Searle, S., Slater, G., Smith, J., Spooner, W., Stabenau, A.,
Stalker, J., Stupka, E., Vastrik, I., & Vidal, A.U., 2002.The Ensembl genome database project,
vol. 30, no. 1, pp.38-41.
Clamp, M., Clarke, L., Curwen, V., Keenan, S., Mongin, S., Potter, S.C., Searle, S.M.J.,
Stabenau, A., & Storey, R., 2004. The Ensembl Analysis Pipeline, vol. 14, no. 5, pp.934-941.
Cox, A.V., Gibbins, B., Hotz, H.R., Meidl, P., Spooner, W., & Stalker, James., 2004. The
Ensembl Web Site: Mechanics of a Genome Browser, vol. 14, no. 5, pp.951-955.
Day, A., Dowell, R.D., Eddy, S.R., Jokerst, R.M., & Stein, L., 2001. The Distributed Annotation
System, vol. 2, no. 7, pp-1-8.
TORIA, 2017. Contacting the Ensembl Helpdesk? Let us know how to reach you. [Online]
ensemble, Available at: http://www.ensembl.info/2017/03/24/contacting-the-ensembl-helpdesk-
let-us-know-how-to-reach-you/
.
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