Functional annotation assigns functions to the genomic elements found by structural annotation, by relating them to biological processes such as the cell cycle, cell death, development, metabolism, etc. It may also be used as an additional quality check by identifying elements that may have been annotated by error. These annotations come in two types, parameter annotations and return type annotations. One large benefit is that they can provide much needed explanation to the reader as to what type a function parameter expects or a function returns. In this example, adding a string explanation to two vague parameters.

1. FUNCTIONAL
ANNOTATION
OF GENOME
SNPANNOTATION
UMER JIBRAN RAZA BSBTM-2020-21
INSTITUTE OF MOLECULAR
BIOLOGY & BIOTECHNOLOGY
BAHAUDDIN ZAKARIYA UNIVERSITY, MULTAN

2. Table of Contents
• Functional Annotation of Genome
• SNP based annotation
• SNP annotation
• Importance
• Tools used in SNP annotation
• Comparison of variants tools
• Retrieval of gene
• Working of different tools

3. Functional Annotation of Genome:
Process of deriving the structural and functional information of a protein or gene from a raw data set
using different analysis tools.
 This method mainly identifies variant function based on the information
 The variant loci are in the known functional region
 Harbor genomic or epigenomic signals.

4. SNP based Annotation:
 Predicting the effect or function of an individual SNP using SNP annotation tools.
 Biological information is extracted
 Collected and displayed in a clear form amenable to query
 SNP functional annotation is typically performed based on the available information on
nucleic acid

5. SNPAnnotation
Classification Bioinformatics
Sub-classification Single Nucleotide Polymorphism
Type of tools used Functional Annotation Tools
Subject Genomic Project

6. Importance of SNPAnnotation
• SNPs role in genome wide association studies, as primary biomarkers
• Marker of choice due to their large numbers in virtually all populations
• Tremendously important in terms of predicting functional significance, genetic mapping and
population genetics
• Annotating large numbers of SNPs is a difficult and complex process
• Need computational methods to handle large dataset
• Majority of SNP annotation tools provide computationally predicted putative deleterious effects
of SNPs
• Tools examine whether a SNP resides in functional genomic regions

7. List of SNP based Annotation Tools
 Notepad++
 Mega_X
 MS Excel
 Ubuntu (Linux based system)
 SnpEff
 PhyreRisk
 Missense3D
 Ensembl VEP
 ANNOVAR
 Jannovar
 PhD-SNP
And many more…………………………………………………………

8. Comparison of variant annotation tools
 A large number of variant annotation tools are available for variant annotation.
 The annotation by different tools does not always agree amongst each other
 rules for data handling differ between applications.
 It is frankly impossible to perform a perfect comparison of the available tools.
 Not all tools have the same input and output nor the same functionality.

9. Retrieve Gene & genomes from Different
websites
Here we study the grain side and width for the analysis to download from mbkbase and NCBI .
Different genes names are obtained after reading different papers on grain size and width.
https://mbkbase.org/rice/customGT
KnownGeneSearch by Symbol
Search by Name
Category Browser
Verified Alleles

10. NCBI
The NCBI houses a series of databases relevant
to biotechnology and biomedicine and is an important resource for
bioinformatics tools and services. Major databases include GenBank for
DNA sequences and PubMed, a bibliographic database for biomedical
literature.
Molecular Breeding Knowledgebase (MBKbase) is a part of the
Strategic Priority Research Program of CAS (class A) for "Molecular
Module-based Designer Breeding Systems". This is a integrated
database which collected population next-generation sequencing,
germplasm resources, phenotypic and various genomics data.
MBKBase

11. Working on GW8
Reported in different papers as (Fine mapping and candidate gene analysis of the quantitative trait
locus gw8.1 associated with grain length in rice, Development of functional markers and
identification of haplotypes for rice grain shape gene GW8., Natural variation in OsMKK3
contributes to grain size and chalkiness in rice.)
Select the rice home

12. It has 5052 base pair sequence
Download the fasta file for the alignment by different tools

13. Install from Play Store
After installing it show the following errors and solve it by
adopting the above procedure
• Change directory (cd)
• /mnt (mount points to removable or temporary files
storage
• Select the folders i.e. cd /users/aaa/downloads
• Spelling are important to put in right way otherwise
it will show error

14. Install the mafft tool by the
command
Sudo apt-get install mafft

15. Aligned by using mafft
• For multiple alignment
• Use linux snpsite for alignment
• For this use Ubuntu software
• By using sudo command of linux
• sudo apt-get install mafft
• mafft --auto --addfragments sample.fasta
reference.fasta > aligned.fasta

16. VCF file produced of the aligned data by the
snp-sites -v -o your_gene.vcf -m -p
aligned.fasta
These are files that we created
from Ubuntu

17. SNPeFF
• SnpEFF database is genetic variant annotation and functional effect prediction toolbox
• Download & install SNPeFF from the Google chrome
• After installation the software it demanded java jar to run into the window
• Select the command line show

18. • Put the command line to build database into the system
• It demands cds, protein, genomes and gene.gff3 files into data

19. A cnfig. File
Put the entry of genome
# rice genome
IRGSP.genome : rice gene

20. Database build here by the following command
snpEff_latest_coresnpEff>java -jar snpeff.jar
build -gff3 -v IRGSP

21. A database has been built

22. Coding & non-coding variants
a. Missense variant
b. Downstream gene variant
c. Upstream gene variant
d. Synonymous variant
e. Stop gained
f. Start gained
g. Intron variant
h. Splice region variant
i. Splice donor variant
j. Nonsense variants

23. Annotation files also created from the vcf files that produced from Ubuntu and run by following
command into
SnpEFF softwaresnpEff_lstest_coresnpEff>
java –jar snpeff.jar IRGSP ./gw8.vcf > gw8.ann.vcf

25. Phenotypically representation

26. THANK YOU