annotation is nothing but the extra informations. the genome annotation is the extra informations about the DNA sequence of the organism. without annotation the squence doesnt make any sense of the sequencing.The current gene prediction methods can be classified into two major categories, abinitio–based and homology-based approaches. The ab initio–based approach predicts genes based on the given sequence alone. The homology-based approach predicts a gene using the alignment of the protein or RNA sequence/ gene models in evolutionary related species.

1. FUNCTIONAL ANNOTATION-
PREDICTION OF GENES
SRIDHARSHINI S
|-M.SC.,BOTANY
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2. WHAT IS ANNOTATION?
•Extra information associated
with any document is called
Annotation.

3. GENOME ANNOTATION
• Genome annotation is also called as DNA Annotation.
• After DNA sequencing, DNA annotation is done.
• The DNA sequence will not make ant sense without annotation.
FROM THIS,
 location of the genes are identified.
 all coding regions of the genes are identified.
 start and stop codons of the genes are identified.
 functions of the gene is identified.

4. TYPES OF GENOME ANNOTATION
• STRUCTURAL ANNOTATION
IDENTIFICATION OF GENOMIC ELEMENTS
1.ORF’s
2. Gene structure
3.location of regulatory regions
4.coding regions
• FUNCTIONAL ANNOTATION
ATTACHING BIOLOGICAL INFORMATION OF THE GENOMIC
ELEMENTS
1.Biological function
2.biochemical function

5. FUNCTIONAL ANNOTATION
•It is the process of attaching biological in
formation to sequence of genes or proteins.
•The basic level of annotations is using
sequence alignment tool BLAST for finding
similarities and then annotating genes or
proteins.

6. • The process of relating crucial biological functions to
the genetic elements as depicted in the structural
annotation step. Biochemical functions, physiological
functions, involved regulations and interactions atop
expressions are some of the critical roles that are
often considered in DNA annotation.
• The above steps can involve biological experiments as
well as in silico analysis mimicking the internal
conditions. A new method seeking to improve
genomics annotation-Proteogenomics is currently in
use, and it utilizes information from expressed
proteins, such information is obtained from mass

7. FUNCTIONAL ANNOTATIONS
• TOOLS USED:
DAVID(Database For Annotation,visualization And Integrated Discovery)
PROSITE
PRINTS
SMART
TIGRFAMs
BLAST2GO
SUPERFAMILY
ProDom
Pfam
Gene3D

8. TYPES OF FUNCTIONAL ANNOTATION
• INDIRECT EVIDENCE OF FUNCTION
expression analysis
structure analysis
sequence analysis
• DIRECT EVIDENCE OF FUNCTION
enzyme assays
binding experiments
pathway analysis
functional complementation
gene mutation

9. APPLICATIONS
• Cancer cell profiling
• Complex disorders
• Depression of genes
• Spontaneous preterm birth
• Genome-wide association studies

10. GENE PREDICTION
• Gene prediction is the process of determining where a coding
gene might be in a genomic sequence.
• Get the exons regions that would be translated to amino acids.
• Functional proteins must begin with a Start codon (where DNA
transcription begins), and end with a Stop codon (where
transcription ends).
• Gene prediction is easy in prokaryotes but difficult in
eukaryotes.why?

11. CATEGORIES OF GENE PREDICTION
PROGRAMS
• The current gene prediction methods can be classified into two
major categories, abinitio–based and homology-based
approaches.
• The ab initio–based approach predicts genes based on the
given sequence alone.
• The homology-based approach predicts a gene using the
alignment of the protein or RNA sequence/ gene models in
evolutionary related species.

12. • The first is the existence of gene signals, which include start
and stop codons, intron splice signals, transcription factor
binding sites, ribosomal binding sites, and polyadenylation
(poly-A) sites. In addition, the triplet codon structure limits the
coding frame length to multiples of three, which can be used as
a condition for gene prediction.
• The homology-based method makes predictions based on
significant matches of the query sequence with sequences of
known genes. For instance, if a translated DNA sequence is
found to be similar to a known protein or protein family from a
database search, this can be strong evidence that the region
codes for a protein. Alternatively, when possible exons of a
genomic DNA region match a sequenced cDNA, this also
provides experimental evidence for the existence of a coding
region.

13. GENE PREDICTION TOOLS
• GeneMark
• HMM (Hidden Markov Model)
• Glimmer (Gene Locator and Interpolated Markov Modeler)
• FGENESB
• RBSfinder

15. THANK YOU