The document discusses several key aspects of gene prediction including:
1. Gene prediction algorithms use signals like start/stop codons, splice sites, and open reading frames to identify genes computationally with near 100% accuracy.
2. There are ab initio, homology-based, and probabilistic models like Hidden Markov Models that can predict prokaryotic and eukaryotic genes.
3. Eukaryotic gene prediction is more challenging due to larger genomes, fewer genes, and intron-exon structures. Programs must consider splicing, polyadenylation, and other post-transcriptional modifications.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
Genome annotation, NGS sequence data, decoding sequence information, The genome contains all the biological information required to build and maintain any given living organism.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Clustal X help to the Bioinformatics candidate to predicts the Multiple Sequence Alignment and Phylogenetic Analysis for given a nuber of Gene Sequences of varrious organism,and find the evolutionary relationship.
If you were looking at an mRNA and saw the codon AUG, what would you .pdfnaveenkumar29100
If you were looking at an mRNA and saw the codon AUG, what would you conclude about it?
What does it mean to that the genetic code is redundant, but not ambiguous? The genetic code is
nearly universal, meaning the same RNA codon that designates tryptophan in humans, designates
tryptophan in bacteria. a. What has this knowledge allowed us to conclude about the code? b.
What has this knowledge allowed us to do with genes Transcription is the DNA-directed
synthesis of RNA: a closer look Describe the general model of transcription. Include in your
answer the steps of transcription and the key elements of each step. Compare and contrast
transcription between prokaryotes and eukaryotes What makes RNA polymerase start
transcribing in a gene at the right place on the DNA of a prokaryotic cell? What makes RNA
polymerase start transcribing in a gene at the right place on the DNA of a eukaryotic cell?
Solution
A)Transcription is the first step in gene expression. It involves copying a gene\'s DNA sequence
to make an RNA molecule.Transcription can be divided into four distinct stages:
Template recognition
Initiation
Elongation
Termination
Initiation:RNA polymerase binds to a sequence of DNA called the promoter,found near the
beginning of a gene.Each gene has its own promoter.Once bound,RNA polymerase separates the
DNA strands,providing the single-stranded template needed for transcription.
Elongation:One strand of DNA,the template strand,acts as a template for RNA polymerase.As it
reads this template one base at a time,the polymerase builds an RNA molecule out of
complementary nucleotides,making a chain that grows from 5\' to 3\'.The RNA transcript carries
the same information as the non-template (coding) strand of DNA,but it contains the base uracil
instead of thymine .
Termination:Sequences called terminators signal that the RNA transcript is complete.Once they
are transcribed,they cause the transcript to be released from the RNA polymerase.
B)Prokaryotes do not have an organized nucleus,so the nuclear materials or DNA is in the
cytoplasm.Therefore,the transcription occurs in the cytoplasm and all the precursors needed for
the transcription are found in the cytoplasm.Prokaryotic transcription requires the RNA
polymerase enzyme in order for the transcription to be successfully completed.The enzyme binds
to the sigma factor and the promoter region,and then initiate the transcription by completing the
holoenzyme.In prokaryotes,DNA is not bound to histones.Thus,the transcription initiates
directly.This could be advantageous when prokaryotes have overlapping genes.Transcription
starts at the promoter region and elongate through the coding region and ends when the RNA
polymerase reads the termination signal.There are two types of termination signals,Rho-
dependent and independant.Transcribed mRNA will be completely translated during the
transcription,and no post-transcription processing will be undergoing most of the
time.Transcriptionl unit has one or more .
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
Open reading frame is part of reading frame that contains no stop codons or region of amino acids coding triple codons.
ORF starts with start codon and ends at stop codon.
INTRODUCTION.
NCBI.
EMBL.
DDBJ.
CONCLUSION.
REFERENSE.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.
The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.
The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature.
All these databases are available online through the Entrez search engine.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Clustal X help to the Bioinformatics candidate to predicts the Multiple Sequence Alignment and Phylogenetic Analysis for given a nuber of Gene Sequences of varrious organism,and find the evolutionary relationship.
If you were looking at an mRNA and saw the codon AUG, what would you .pdfnaveenkumar29100
If you were looking at an mRNA and saw the codon AUG, what would you conclude about it?
What does it mean to that the genetic code is redundant, but not ambiguous? The genetic code is
nearly universal, meaning the same RNA codon that designates tryptophan in humans, designates
tryptophan in bacteria. a. What has this knowledge allowed us to conclude about the code? b.
What has this knowledge allowed us to do with genes Transcription is the DNA-directed
synthesis of RNA: a closer look Describe the general model of transcription. Include in your
answer the steps of transcription and the key elements of each step. Compare and contrast
transcription between prokaryotes and eukaryotes What makes RNA polymerase start
transcribing in a gene at the right place on the DNA of a prokaryotic cell? What makes RNA
polymerase start transcribing in a gene at the right place on the DNA of a eukaryotic cell?
Solution
A)Transcription is the first step in gene expression. It involves copying a gene\'s DNA sequence
to make an RNA molecule.Transcription can be divided into four distinct stages:
Template recognition
Initiation
Elongation
Termination
Initiation:RNA polymerase binds to a sequence of DNA called the promoter,found near the
beginning of a gene.Each gene has its own promoter.Once bound,RNA polymerase separates the
DNA strands,providing the single-stranded template needed for transcription.
Elongation:One strand of DNA,the template strand,acts as a template for RNA polymerase.As it
reads this template one base at a time,the polymerase builds an RNA molecule out of
complementary nucleotides,making a chain that grows from 5\' to 3\'.The RNA transcript carries
the same information as the non-template (coding) strand of DNA,but it contains the base uracil
instead of thymine .
Termination:Sequences called terminators signal that the RNA transcript is complete.Once they
are transcribed,they cause the transcript to be released from the RNA polymerase.
B)Prokaryotes do not have an organized nucleus,so the nuclear materials or DNA is in the
cytoplasm.Therefore,the transcription occurs in the cytoplasm and all the precursors needed for
the transcription are found in the cytoplasm.Prokaryotic transcription requires the RNA
polymerase enzyme in order for the transcription to be successfully completed.The enzyme binds
to the sigma factor and the promoter region,and then initiate the transcription by completing the
holoenzyme.In prokaryotes,DNA is not bound to histones.Thus,the transcription initiates
directly.This could be advantageous when prokaryotes have overlapping genes.Transcription
starts at the promoter region and elongate through the coding region and ends when the RNA
polymerase reads the termination signal.There are two types of termination signals,Rho-
dependent and independant.Transcribed mRNA will be completely translated during the
transcription,and no post-transcription processing will be undergoing most of the
time.Transcriptionl unit has one or more .
Disclaimer: This is not my own Powerpoint Presentation. Credits to Mindanao State University - General Santos City - College of Natural Science and Mathematics.
Protein synthesis is the process whereby biological cells generate new proteins. Translation, the assembly of amino acids by ribosomes, is an essential part of the biosynthetic pathway, along with generation of messenger RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-translational transport, and post-translational modification. Protein biosynthesis is strictly regulated at multiple steps. They are principally during transcription (phenomenon of RNA synthesis from DNA template) and translation (phenomenon of amino acid assembly from RNA). The cistron DNA is transcribed into the first of a series of RNA intermediates. The last version is used as a template in synthesis of a polypeptide chain. Protein will often be synthesized directly from genes by translating mRNA. A proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis during post translational modification. A preprotein is a form that contains a signal sequence (an N-terminal signal peptide) that specifies its insertion into or through membranes, i.e., targets them for secretion. The signal peptide is cleaved off in the endoplasmic reticulum. Preproteins have both sequences (inhibitory and signal) still present. In protein synthesis, a succession of tRNA molecules charged with appropriate amino acids are brought together with an mRNA molecule and matched up by base-pairing through the anti-codons of the tRNA with successive codons of the mRNA. The amino acids are then linked together to extend the growing protein chain, and the tRNAs, no longer carrying amino acids, are released. This whole complex of processes is carried out by the ribosome, formed of two main chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. The ribosome latches onto the end of an mRNA molecule and moves along it, capturing loaded tRNA molecules and joining together their amino acids to form a new protein chain.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
2. Gene:
• Asequence of nucleotides coding for protein.
CentralDogma:
• Proposed in 1958 by Francis Crick.
• Hepostulated that all possibleinformation
transferred, are not viable.
• Hepublished apaper in 1970.
CODONS:
• Discovered by Sydney Brenner and Francis Crickin
1961.
• In every triplet of nucleotides, each codoncodesfor
one amino acid in aprotein.
3. DNA RNA PROTEIN PHENOTYPE
2
4
cDNA
1 3
1. TRANSCRIPTION
2. TRANSLATION
3. GENE EXPRESSION
4. REVERSETRANSCRIPTION
4. DEfiniTION
• It is aprerequisite for detailed functionalannotation
of genesand genomes.
• It candetect location of ORFs(Open Reading
Frames), structures of introns andexons.
• It describes all the genescomputationally withnear
100% accuracy.
• It canreduce the amount ofexperimental
verification work required.
5. TYPES
• Abinitio- gene signals, intron splice, transcription
factor binding site, ribosomal binding site, poly-
adenylation site, triplet codon structure and gene
content.
• Homology- significant matches of query sequence
with sequence of knowngenes.
• Probabilistic models like Markov model or Hidden
Markov Models (HMMs).
Abinitio-based
Homology-
based
7. Prokaryoticgene
prediction
• Geneprediction is easier in microbialgenomes.
• Smaller genomes, high gene density, very few
repetitive sequence, more sequenced genomes.
• Start codon is ATG.
• Ribosomal binding site/Shine Dalgarno sequence.
8. Openreadingframes
• A sequence defined by in-frame start and stop
codon, which in turn defines aputative amino acid
sequence.
• Agenome of length n is comprised of (n/3)codons.
• Stop codons break genome into segments between
consecutive stop codons.
• Thesub-segments of these that start from the Start
codon (ATG)areORFs.
• DNA is translated in all six possible frames,
three frames forward and three reverse.
ATG TGA
Genomic Sequence
Open reading frame
10. Probabilisticmodels
• Statistical description of agene.
• Markov Models &Hidden Markov Models.
• Usedto distinguish oligonucleotide distributions in
the coding regions from those for non-coding
regions.
• Probability of distribution of nucleotides inDNA
sequence depends on the order k.
• Typesof order- zero,first and second.
• Order , gene canpredicted more accurately.
11. Genecontent and length distribution of
prokaryotic genes
TYPICAL ATYPICAL
Ranges from100
to 500amino
acids with a
nucleotide
distribution
typical ofthe
organism.
Shorter or longer
with different
nucleotidestatistics.
Genes tend toescape
detection when
typical gene modelis
used.
12. Genefindingprogramsin
prokaryotes
• Theprograms are based on HMM/IMM.
GeneMark.hmm (microbial genomes)
Glimmer (UNIX program from TIGR). Computation
involves two steps viz. model building & gene
prediction.
FGENESB (bacterial sequences). It uses Vertibi
algorithm & linear discriminant analysis(LDA).
RBSfinder- Searches from ribosomal binding site or
shine dalgarno sequence for prediction of translation
initiation site.
13. Sensitivity Ability to include correct predictions. It is the
fraction of known genescorrectlypredicted.
Specificity Ability to exclude incorrect predictions. It is the
fraction of predicted genes that correspond to true genes.
Both are the proportion of true signals.
14. Eukaryoticgeneprediction
• Genomes are much larger than prokaryotes(10Mbp to
670 Gbp).
• Low gene density.
• Spacebetween genesis very large and rich in
repetitive sequences & transposableelements.
• Splitting of genesby intervening noncodingsequences
(introns) and joining of coding sequences(exons).
15. • Splice junctions follow GT-AGrule.
• An intron at the 5’ splice junction hasaconsensus
motif GTAAGTand that at 3’ endNCAG.
exon 1 exon 2
• Geneshave ahigh density of CGdinucleotides near
the transcription start site. Thisregion is CpGisland. It
helps to identify the transcription initiation site of an
eukaryotic gene.
• Somepost-transcriptional modification occur with the
transcript to become mature mRNAviz. Capping,
Splicing and Polyadenylation.
Acceptor
Site
Donor
Site
GT AG
16. o CAPPING: Occurs at the 5’ end of the transcript. It
involves methylation at the initial residue of the
RNA.
o SPLICING: Processof removal of intronsand
joining of exons. It involves alargeRNA-protein
complex called spliceosome.
o POLYADENYLATION:Addition of astretch ofAs
(~250) at the 3’ end of the RNA.Theprocessis
accomplished by poly-Apolymerase.
17. Genefindingprogramsin
EUkaryotes
• Three categories of algorithms
Ab Initiobased-
It joins the exonsin correct order.Twosignals->
a) Genesignals: asmall pattern within the genomic
DNAincluding putative splice sites, start and stop
sites of transcription or translation, branchpoints,
transcription factor binding sites, recognizable
consensus sequences.
b) Genecontent: aregion of genomic DNAincluding
nucleotide and amino acid distribution, Synonymous
codon usageand hexamer frequencies.
18. Neural network based algorithm
-Composed of network of mathematicalvariables.
-Multiple layers like input, output and hiddenlayers.
-GRAIL (Splice junctions, start and stop codons, poly-A
sites, promoters and CpGislands). It scansthe query
sequence with windows of variable lengths &scores.
Discriminant analysis
-Linear Discriminant Analysis (LDA) represents 2D
graph of coding signals vs. all possible 3’ splice site
positions; adiagonal line.
-Quadratic DiscriminantAnalysis (QDA)represents
quadratic function; acurved line.
-FGENES (LDA)
19. -FGENESH [Find Genes] (HMMs)
-FGENESH_C (Similarity based)
-FGENESH+ (Combination of ab initio &similarity
based)
-MZEF [Michael Zhang’s Exon Finder](QDA)
HMMs
-GENSCAN (Fifth order HMMs); combination of
hexamer frequencies with coding signals;probability
score P>0.5
-HMMgene (Conditional Maximum Likelihood);
combination of ab initio & homology-basedalgorithm
20. Homology-based-
Exonstructures and sequencesof related speciesare
highly conserved.
Comparison of homologous sequences derived from
cDNAor ExpressedSequenceTags (ESTs).
-GenomeScan (Combination of GENSCANprediction
results with BLASTXsimilaritysearches)
-EST2Genome (Intron-exon boundaries); Comparison
of an ESTsequence with agenomic DNAsequence
-SGP-1 [Syntenic Gene Prediction] (Similar to EST2)
-TwinScan (gene-finding server; similar to
GenomeScan)
21. Consensus-based-
Combination of results of multiple programsbased
on consensus.
Improvement of specificity by correctingfalse
positives & problem ofoverprediction.
Lowered sensitivity & missedpredictons.
-GeneComber (Combination of HMMgene&
GenScanprediction results)
-DIGIT (Combination of FGENESH,GENSCAN&
HMMgene)
22. GENE EXPRESSION
Two steps are required
1. Translation
The synthesis of a polypeptide chain using the genetic
code on the mRNA molecule as its guide.
1. Transcription
The synthesis of mRNA uses the gene on the DNA
molecule as a template
This happens in the nucleus of eukaryotes
23. Types OF RNA
Messenger RNA (mRNA) <5%
Ribosomal RNA (rRNA) Up to 80%
Transfer RNA (tRNA) About 15%
In eukaryotes small nuclear ribonucleoproteins (snRNP aka
spliceosomes
Structural characteristics of RNA molecules
Single polynucleotide strand which may be looped or
coiled (not a double helix)
Sugar Ribose (not deoxyribose)
Bases used: Adenine, Guanine, Cytosine and Uracil (not
Thymine
24. Transcription: The synthesis of a strand of mRNA (and
other RNAs)
Uses an enzyme RNA polymerase
Proceeds in the same direction as replication (5’ to 3’)
Forms a complementary strand of mRNA
It begins at a promotor site, which signals that the beginning of
the gene is near (about 20 to 30 nucleotides away)
After the end of the gene is reached, there is a terminator
sequence that tells RNA polymerase to stop transcribing
NB Terminator sequence ≠ terminator codon
RNA POLYMERASE
25. Editing the mRNA
In prokaryotes, transcribed mRNA
goes straight to the ribosomes in the
cytoplasm
In eukaryotes, freshly transcribed
mRNA in the nucleus is about 5000
nucleotides long
When the same mRNA is used for
translation at the ribosome it is only
1000 nucleotides long
The mRNA has been edited
The parts which are kept for gene
expression are called EXONS (exons =
expressed)
The parts which are edited out (by
spliceosomes) are called INTRONS.