Genome annotation is the process of analyzing genomic DNA sequences to extract biological meaning and context. It involves two main steps - structural annotation, which locates gene elements like exons and introns, and functional annotation, which predicts the functions of gene products. Computational tools are crucial given the vast amounts of sequence data. They use various approaches like identifying open reading frames, conserved sequences, statistical patterns and sequence similarities to model gene structures and infer functions. The results are then integrated into automated annotation pipelines to generate comprehensive and reliable gene annotations for genomes.
This document discusses gene prediction and promoter prediction. It begins by explaining that gene prediction involves locating protein-coding genes within sequenced genomes in order to understand their functional content. Various computational methods are used for gene prediction, including searching for signals like start/stop codons, searching coding content, and comparing sequences to find homologs. Promoter prediction involves locating DNA elements that regulate gene expression and is challenging due to diversity and short, conserved motifs. Ab initio and comparative phylogenetic footprinting methods are used to predict promoters and regulatory elements in prokaryotes and eukaryotes.
BTC 506 Gene Identification using Bioinformatic Tools-230302130331.pptxChijiokeNsofor
This document discusses several bioinformatics tools and methods for identifying genes from genomic sequences, including:
1. Obtaining sequence data through sequencing technologies and preprocessing data.
2. Using tools like Ensembl, RefSeq and UCSC Genome Browser for gene identification and annotation.
3. Using gene prediction tools like Augustus, GeneMark and Glimmer to predict gene locations and structures.
4. Validating predicted genes through comparison to known genes or experimental validation with RNA-seq or RT-PCR.
This document discusses various bioinformatics tools and methods for identifying genes from genomic sequences. It begins by defining genes and genomes, then describes reference databases like RefSeq that are important for gene identification. It outlines the general workflow for gene identification, including obtaining sequences, preprocessing, annotation, prediction, and validation. Specific tools mentioned include GENSCAN, Glimmer, and Augustus for gene prediction, and BLAST for sequence alignment. The document also discusses identifying other genomic features like promoters, repeats, and open reading frames. It emphasizes that accurate gene identification requires both computational and experimental approaches.
The document provides information about various bioinformatics tools for DNA sequence analysis. It describes tools for finding protein coding regions like GeneMark and GENSCAN. It discusses tools for predicting promoters like SoftBerry Promoter and Promoter 2.0. It outlines how Tandem Repeat Finder can detect tandem repeats and how RepeatMasker can mask interspersed repeats in a sequence. It also discusses UTRScan for finding UTR locations and CpG Islands for detecting CpG islands. For each tool, it provides the procedure and interpretation of sample results.
The document discusses genomics and comparative genomics. It defines genomics as the study of genomes and notes that comparative genomics compares two or more genomes to discover similarities and differences. Comparative genomics can provide insights into evolutionary biology, drug discovery, gene function prediction, and identification of genes and regulatory elements. The document outlines different levels of genome comparison including nucleotide statistics, genome structure at the DNA and gene levels, and describes various methods used in comparative genomic analyses.
This document provides an introduction and overview of manual genome annotation using the Apollo genome annotation tool. It begins with an outline of the webinar topics, which include an introduction to manual annotation and its necessity, an overview of the Apollo tool and its functionality for collaborative curation, and examples and demonstrations. The document then covers key concepts for manual annotation such as the definition of a gene, genome curation steps, transcription and translation including reading frames, splice sites, and phase. The goal of the webinar is to help participants better understand genome curation and manual annotation using Apollo to identify and modify gene models.
This document summarizes different computational strategies for predicting genes in eukaryotic organisms. It discusses four generations of gene prediction programs that have been developed, from first generation programs that identified coding regions to current programs that can predict full gene structures. Two main classes of gene prediction methods are described: sequence similarity-based methods that use homology searches, and ab initio methods that use signals and hidden Markov models to predict genes without prior sequence information. Several specific gene prediction programs are outlined, including AUGUSTUS, GENSCAN, GENEID, GENIE, and EUGENE.
This document discusses gene prediction and promoter prediction. It begins by explaining that gene prediction involves locating protein-coding genes within sequenced genomes in order to understand their functional content. Various computational methods are used for gene prediction, including searching for signals like start/stop codons, searching coding content, and comparing sequences to find homologs. Promoter prediction involves locating DNA elements that regulate gene expression and is challenging due to diversity and short, conserved motifs. Ab initio and comparative phylogenetic footprinting methods are used to predict promoters and regulatory elements in prokaryotes and eukaryotes.
BTC 506 Gene Identification using Bioinformatic Tools-230302130331.pptxChijiokeNsofor
This document discusses several bioinformatics tools and methods for identifying genes from genomic sequences, including:
1. Obtaining sequence data through sequencing technologies and preprocessing data.
2. Using tools like Ensembl, RefSeq and UCSC Genome Browser for gene identification and annotation.
3. Using gene prediction tools like Augustus, GeneMark and Glimmer to predict gene locations and structures.
4. Validating predicted genes through comparison to known genes or experimental validation with RNA-seq or RT-PCR.
This document discusses various bioinformatics tools and methods for identifying genes from genomic sequences. It begins by defining genes and genomes, then describes reference databases like RefSeq that are important for gene identification. It outlines the general workflow for gene identification, including obtaining sequences, preprocessing, annotation, prediction, and validation. Specific tools mentioned include GENSCAN, Glimmer, and Augustus for gene prediction, and BLAST for sequence alignment. The document also discusses identifying other genomic features like promoters, repeats, and open reading frames. It emphasizes that accurate gene identification requires both computational and experimental approaches.
The document provides information about various bioinformatics tools for DNA sequence analysis. It describes tools for finding protein coding regions like GeneMark and GENSCAN. It discusses tools for predicting promoters like SoftBerry Promoter and Promoter 2.0. It outlines how Tandem Repeat Finder can detect tandem repeats and how RepeatMasker can mask interspersed repeats in a sequence. It also discusses UTRScan for finding UTR locations and CpG Islands for detecting CpG islands. For each tool, it provides the procedure and interpretation of sample results.
The document discusses genomics and comparative genomics. It defines genomics as the study of genomes and notes that comparative genomics compares two or more genomes to discover similarities and differences. Comparative genomics can provide insights into evolutionary biology, drug discovery, gene function prediction, and identification of genes and regulatory elements. The document outlines different levels of genome comparison including nucleotide statistics, genome structure at the DNA and gene levels, and describes various methods used in comparative genomic analyses.
This document provides an introduction and overview of manual genome annotation using the Apollo genome annotation tool. It begins with an outline of the webinar topics, which include an introduction to manual annotation and its necessity, an overview of the Apollo tool and its functionality for collaborative curation, and examples and demonstrations. The document then covers key concepts for manual annotation such as the definition of a gene, genome curation steps, transcription and translation including reading frames, splice sites, and phase. The goal of the webinar is to help participants better understand genome curation and manual annotation using Apollo to identify and modify gene models.
This document summarizes different computational strategies for predicting genes in eukaryotic organisms. It discusses four generations of gene prediction programs that have been developed, from first generation programs that identified coding regions to current programs that can predict full gene structures. Two main classes of gene prediction methods are described: sequence similarity-based methods that use homology searches, and ab initio methods that use signals and hidden Markov models to predict genes without prior sequence information. Several specific gene prediction programs are outlined, including AUGUSTUS, GENSCAN, GENEID, GENIE, and EUGENE.
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.
This document discusses gene identification and genome annotation. It describes how gene finding in eukaryotes is difficult due to smaller percentages of genes in genomes like humans, and larger intron sizes. It covers open reading frames, complications with introns, and the use of six-frame translation to find protein coding sequences. Software tools for structural and functional annotation are outlined, including identifying genes through homology searching and ab initio prediction using hidden Markov models. The accuracy challenges of ab initio prediction are also summarized.
1. Artificial neural networks (ANNs) are being used as a bioinformatics approach for gene prediction and genetic diversity analysis. ANNs consist of interconnected layers that learn from input to output.
2. For gene prediction, a neural network is constructed with multiple input, hidden, and output layers. The input is a gene sequence and output is exon probability. Weights between layers are adjusted during training to recognize patterns.
3. ANNs have advantages over traditional statistical methods as they can model more complex data relationships without requiring detailed system information. Different ANN types exist for various applications in bioinformatics.
Apollo: A workshop for the Manakin Research Coordination NetworkMonica Munoz-Torres
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
This document discusses functional genomics and different methods for analyzing gene expression at the whole genome level. Functional genomics focuses on determining gene functions through high-throughput experimental approaches. Two main methods described are sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. Microarrays allow analysis of thousands of genes simultaneously through hybridization of fluorescently-labeled cDNA to probes on a chip, while ESTs and SAGE involve sequencing of cDNA fragments to determine expression levels. Both methods aim to provide information on overall gene expression patterns in a genome under different conditions.
SAGE- Serial Analysis of Gene ExpressionAashish Patel
Serial Analysis of Gene Expression (SAGE) is a method to quantify gene expression in cells. It involves extracting short sequence tags from mRNA transcripts and concatenating them for efficient sequencing. This allows simultaneous analysis of thousands of transcripts. SAGE provides quantitative gene expression data without prior knowledge of genes and can identify differentially expressed genes between cell types or conditions. While powerful, it requires substantial sequencing and computational analysis of large datasets.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
This document discusses functional genomics and its approaches. It defines functional genomics as the worldwide experimental approach to access the function of genes by using information from structural genomics. The key functional genomics approaches discussed are transcriptomics, proteomics, metabolomics, interactomics, epigenetics, and nutrigenomics. Modern techniques discussed include expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and microarray analysis.
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
The document discusses genome assembly and gene prediction from sequencing data. It describes how short DNA sequence reads are assembled into longer contiguous sequences or contigs. It also explains different approaches used for gene prediction, including ab initio prediction using statistical models, homology-based prediction using known genes from related organisms, and transcript-based prediction using cDNA or RNA-seq data. Key steps involve repeat masking, identifying open reading frames, and dealing with complications from introns in eukaryotic genomes. The challenges of gene prediction and determining which predictions are correct are also addressed.
Bioinformatics uses computers to store, organize, and analyze biological data, particularly DNA and protein sequences. Key data types include DNA, RNA, and protein sequences, as well as data from experiments like transcriptomics and proteomics. Common analyses include sequence comparisons and searches for coding regions. DNA contains genetic information encoded as sequences of nucleotides that are read from 5' to 3'. It is double-stranded and antiparallel. Genes encode proteins through transcription of DNA to mRNA and translation of mRNA to protein.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
International Journal of Engineering Research and DevelopmentIJERD Editor
This document discusses a study that uses the ke-REM (ke-Rule Extraction Method) classifier to predict promoter regions in DNA sequences. The study evaluates the performance of ke-REM compared to existing promoter prediction techniques. ke-REM constructs rules based on attribute-value pairs from a dataset of 106 E. coli DNA sequences, each containing 57 nucleotides. The results show that ke-REM competes well with existing methods for identifying promoter regions in DNA.
This document discusses gene prediction and some of the computational challenges involved. It covers topics like genes and proteins, gene prediction problems, computational approaches like using open reading frames and codon usage. It also discusses central dogma, exons, introns, splicing signals, genetic code and different gene prediction algorithms.
This document discusses gene prediction and some of the computational challenges involved. It covers topics like genes and proteins, gene prediction problems, computational approaches like using open reading frames and codon usage. It also discusses central dogma, exons, introns, splicing signals, genetic code and stop codons. Popular gene prediction algorithms like GENSCAN and TWINSCAN that use hidden Markov models and similarity are also mentioned.
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
This document summarizes the key steps in processing raw single-cell RNA sequencing (scRNA-seq) data, including:
1. Aligning reads to a reference genome or transcriptome using tools like STAR or HISAT2.
2. Counting reads and assigning them to genes, which can involve splitting counts between overlapping genes.
3. Normalizing counts within samples using transcripts per million (TPM) for downstream analysis.
4. Identifying cell barcodes and unique molecular identifiers (UMIs) to assign reads to cells and collapse PCR duplicates.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
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.
This document discusses gene identification and genome annotation. It describes how gene finding in eukaryotes is difficult due to smaller percentages of genes in genomes like humans, and larger intron sizes. It covers open reading frames, complications with introns, and the use of six-frame translation to find protein coding sequences. Software tools for structural and functional annotation are outlined, including identifying genes through homology searching and ab initio prediction using hidden Markov models. The accuracy challenges of ab initio prediction are also summarized.
1. Artificial neural networks (ANNs) are being used as a bioinformatics approach for gene prediction and genetic diversity analysis. ANNs consist of interconnected layers that learn from input to output.
2. For gene prediction, a neural network is constructed with multiple input, hidden, and output layers. The input is a gene sequence and output is exon probability. Weights between layers are adjusted during training to recognize patterns.
3. ANNs have advantages over traditional statistical methods as they can model more complex data relationships without requiring detailed system information. Different ANN types exist for various applications in bioinformatics.
Apollo: A workshop for the Manakin Research Coordination NetworkMonica Munoz-Torres
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
This document discusses functional genomics and different methods for analyzing gene expression at the whole genome level. Functional genomics focuses on determining gene functions through high-throughput experimental approaches. Two main methods described are sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. Microarrays allow analysis of thousands of genes simultaneously through hybridization of fluorescently-labeled cDNA to probes on a chip, while ESTs and SAGE involve sequencing of cDNA fragments to determine expression levels. Both methods aim to provide information on overall gene expression patterns in a genome under different conditions.
SAGE- Serial Analysis of Gene ExpressionAashish Patel
Serial Analysis of Gene Expression (SAGE) is a method to quantify gene expression in cells. It involves extracting short sequence tags from mRNA transcripts and concatenating them for efficient sequencing. This allows simultaneous analysis of thousands of transcripts. SAGE provides quantitative gene expression data without prior knowledge of genes and can identify differentially expressed genes between cell types or conditions. While powerful, it requires substantial sequencing and computational analysis of large datasets.
This document provides an overview of functional genomics and methods for transcriptome analysis. It discusses two main approaches - sequence-based approaches like expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE), and microarray-based approaches. For sequence-based approaches, it describes how ESTs can provide gene discovery and expression information but have limitations. It outlines the SAGE methodology and gene index construction to organize EST data. For microarrays, it summarizes the basic workflow including sample preparation, hybridization, image analysis and data normalization to identify differentially expressed genes through statistical tests.
This document discusses functional genomics and its approaches. It defines functional genomics as the worldwide experimental approach to access the function of genes by using information from structural genomics. The key functional genomics approaches discussed are transcriptomics, proteomics, metabolomics, interactomics, epigenetics, and nutrigenomics. Modern techniques discussed include expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and microarray analysis.
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
The document discusses genome assembly and gene prediction from sequencing data. It describes how short DNA sequence reads are assembled into longer contiguous sequences or contigs. It also explains different approaches used for gene prediction, including ab initio prediction using statistical models, homology-based prediction using known genes from related organisms, and transcript-based prediction using cDNA or RNA-seq data. Key steps involve repeat masking, identifying open reading frames, and dealing with complications from introns in eukaryotic genomes. The challenges of gene prediction and determining which predictions are correct are also addressed.
Bioinformatics uses computers to store, organize, and analyze biological data, particularly DNA and protein sequences. Key data types include DNA, RNA, and protein sequences, as well as data from experiments like transcriptomics and proteomics. Common analyses include sequence comparisons and searches for coding regions. DNA contains genetic information encoded as sequences of nucleotides that are read from 5' to 3'. It is double-stranded and antiparallel. Genes encode proteins through transcription of DNA to mRNA and translation of mRNA to protein.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
International Journal of Engineering Research and DevelopmentIJERD Editor
This document discusses a study that uses the ke-REM (ke-Rule Extraction Method) classifier to predict promoter regions in DNA sequences. The study evaluates the performance of ke-REM compared to existing promoter prediction techniques. ke-REM constructs rules based on attribute-value pairs from a dataset of 106 E. coli DNA sequences, each containing 57 nucleotides. The results show that ke-REM competes well with existing methods for identifying promoter regions in DNA.
This document discusses gene prediction and some of the computational challenges involved. It covers topics like genes and proteins, gene prediction problems, computational approaches like using open reading frames and codon usage. It also discusses central dogma, exons, introns, splicing signals, genetic code and different gene prediction algorithms.
This document discusses gene prediction and some of the computational challenges involved. It covers topics like genes and proteins, gene prediction problems, computational approaches like using open reading frames and codon usage. It also discusses central dogma, exons, introns, splicing signals, genetic code and stop codons. Popular gene prediction algorithms like GENSCAN and TWINSCAN that use hidden Markov models and similarity are also mentioned.
description of functional genomics and structural genomics and the techniques involved in it and also decribing the models of forward genetics and techniques involved in it and reverse genetics and techniques involved in it
This document summarizes the key steps in processing raw single-cell RNA sequencing (scRNA-seq) data, including:
1. Aligning reads to a reference genome or transcriptome using tools like STAR or HISAT2.
2. Counting reads and assigning them to genes, which can involve splitting counts between overlapping genes.
3. Normalizing counts within samples using transcripts per million (TPM) for downstream analysis.
4. Identifying cell barcodes and unique molecular identifiers (UMIs) to assign reads to cells and collapse PCR duplicates.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
Mending Clothing to Support Sustainable Fashion_CIMaR 2024.pdfSelcen Ozturkcan
Ozturkcan, S., Berndt, A., & Angelakis, A. (2024). Mending clothing to support sustainable fashion. Presented at the 31st Annual Conference by the Consortium for International Marketing Research (CIMaR), 10-13 Jun 2024, University of Gävle, Sweden.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
2. Definition:
It is the process of taking the raw DNA sequence
produced by the genome-sequencing projects and
adding the layers of analysis and interpretation
necessary to extract its biological significance and
place it into the context of our understanding of
biological processes.
3. • Today, the public international sequence databases contain
more than nine billion nucleotides and the flow of new
sequences is increasing dramatically. For scientists, the
challenge is to exploit this huge amount of sequences.
• To extract biological knowledge from anonymous genomic
sequences is the main objective of genome annotation.
• The extensive use of computer tools is needed to minimize
the slow and costly human interventions. This is the reason
why annotation is often synonymous with prediction.
• The annotation work is divided into two steps: structural
annotation, which consists mainly of localizing gene elements;
and functional annotation, which aims at assigning a
biochemical function to the deduced gene products.
4. Structural annotation
The prediction of the gene elements is a complex problem
and its issue is primordial because of its consequences on all
the following analyses.
• Eukaryotic genes with their mosaic structure are more difficult
to find than prokaryotic ones which are simple open reading
frames. The presence of introns complicates the problem,
although the binding sites of the spliceosome may be used to
predict the exact position of the exon borders.
• According to the prediction tools, the result of the prediction
concerns the splice sites, the exons or the whole gene (gene
modelling software).
5. Gene prediction in Prokaryotes
• Prokaryotes have relatively small genomes with sizes ranging
from 0.5 to 10 Mbp.
• But gene density in the genomes is high with more than 90%
of a genome sequence containing coding sequence.
• In bacteria majority of genes start with ATG which codes for
methionine. Occasionally, GTG and TTG are used as
alternative start codons. These codons not necessarily give a
clear indication of the translation initiation site. This is
overcome by the presence of Shine- Delgarno sequence,
which is a stretch of purine rich sequence complementary to
16S rRNA in the ribosome.
• Many genes are transcribed together as one operon.
The end of the operon is characterized by a transcription
termination signal called rho- independent terminator.
6. Conventional determination of ORFs
• One method is based on the nucleotide composition of the
third position of codon. It has been observed that this
position has a preference to use G or C over A or T.
• By plotting the GC composition at this position, regions with
values significantly above the random level can be identified,
which are indicative of the presence of ORFs.
• There is a similar method called TESTCODE that exploits the
fact that the third codon nucleotides in a coding region tend
to repeat themselves.
7. Performance evaluation
• Accuracy can be described by evaluating two parameters such
as sensitivity and specificity. To describe this concept four
features are used: true positive (TP), false positive (FP), false
negative (FN), true negative (TN).
• TP: correctly predicted feature
• FP: incorrectly predicted feature
• FN: missed feature
• TN: correctly predicted absence of a feature
• Sensitivity is the proportion of true signals predicted among
all possible true strengths.
• Specificity is the proportion of true signals among all signals
that are predicted.
Sn = TP/(TP+FN)
SP = TP/(TP+FP)
9. Gene prediction in eukaryotes
• Eukaryotic nuclear genomes are much larger than prokaryotic
ones, with size ranging from 10 Mbp to 670 Gbp.
• They tend to have a very low gene density. For example in
humans only 3% of the genome codes for genes, with about 1
gene per 100 kbp on average.
• The nascent mRNA undergoes post -transcriptional
modification before becoming a mature mRNA for protein
translation.
• The main issue in prediction of eukaryotic genes is the
identification of exons, introns and splicing sites.
10. Prediction can be made on the basis of :
• Presence of conserved sequences - Splice junctions of introns and
exons follow the GT-AG rule.
• Statistical patterns- Nucleotide compositions and codon bias in
coding regions of eukaryotes are different from those of the non
coding regions
Most vertebrate genes use ATG as the translation start codon and
have uniquely conserved sequences called as Kozak sequence
(CCGCCATGG)
• Presence of CpG island- Most of these genes have a high density of
CG dinucleotides near the transcription start site. Here ‘p’ refers to
the phosphodiester bond between the two nucleotides.
11. Gene prediction programs
Ab initio-based programs:
• This discriminate exons from non coding sequences and
subsequently joins them together in the correct order.
• It rely on two features gene signals and gene content.
• In addition with HMMs, discriminant analysis ,neural network
based algorithms are also used in gene prediction.
12. • Neural networks:
It is a statistical
model with a special architecture
for pattern recognition
and classification. Here multiple
layers are constructed- input,
output and hidden layers. The
output is the probability of the
exon structure. GRAIL is a
program based on neural
network algorithm. Fig: Architecture of a neural
network for eukaryotic gene
prediction
13. • Prediction using HMMs:
- GENSCAN is a web based program on fifth- order HMMs,
- HMMgene is also a web program. It uses a criterion called
the conditional maximum likelihood to discriminate coding
from non coding features.
• Prediction using Discriminant Analysis:
- Some gene prediction algorithms rely on discriminant
analysis, either LDA or quadratic discriminant analysis (QDA).
- LDA works by plotting a 2-D graph of coding signals versus all
potential 3’ splice site positions and drawing a diagonal line
that best separates coding signals from non-coding signals
based on knowledge learned from training data sets of known
gene structures.
14. - QDA draws a curved line based on a quadratic function to
separate coding and non-coding features.
Programs used are: FGENES, FGENESH, FGENESH_C,
FGENESH+,MZEF
Homolgy based programs:
- These are based on the fact that exon structures and exon
sequences of related species are highly conserved.
15. - When coding frames in a query sequence are translated and
used to align with closest protein homologs found in
database, nearly perfectly matched regions can be used to
reveal the exon boundaries in the query.
- Programs used are:
GenomeScan, EST2Genome, SGP-1, TwinScan
• Consensus based programs:
These programs are developed using consensus- based
algorithms which combine results of multiple programs based
on consensus. However this may lead to lowered sensitivity
and missed predictions.
Eg of consensus- based programs are: GeneComber, DIGIT
16. Functional annotation
• At the present time, the functional genome annotation is
based on the idea that some sequence similarities detected
between two proteins mean that they are homologs i.e. they
come from the same ancestor and share the same
biochemical function.
• Therefore, for each predicted gene, the protein is deduced
from the coding region and is compared through BlastP with
the protein databases.
• If the similarities detected are considered relevant, the name
(function) of the putative homologue protein is associated
with the prediction.
17. • The tendency is nevertheless the following:
when a predicted gene product is 100 % identical to an
already characterized protein, it receives the same name,
whereas sequences with stringent similarity to known
proteins are called ‘putative’ proteins of the same name.
• The sequences for which only similarities to ESTs are detected
and named ‘unknown’ proteins.
• Finally, genes without similar sequences and, hence, only
deduced from intrinsic prediction programs are labelled
‘hypothetical’.
• Some annotators confirm and complete the Blast results by
full-length alignments between the query protein and the
closest homologue detected, and by looking for motifs and
family signatures.
18. Automatic genome annotation
pipelines
• The primary goal of the pipeline process is to deliver highly
accurate and reliable genome annotations, using the widest
possible range of evidence from available databases.
• As pipelines have evolved, the trend has been to move away
from single algorithm methods and towards consensus-based
approaches.
• Pipelines are the integration of suites of bioinformatics
software tools with multiple databases, to manage
automatically the analysis and storage of genomic sequence.
• Genomic sequences pass through several successive levels of
algorithms. Each layer of processing provides further
refinement of annotation detail.
19. Fig: The generic structure of an automatic genome annotation pipeline
and delivery system.
20. Genomic pipelines:
Several genomic pipelines exist worldwide. Publicly funded
projects include
• Ensembl at the European Bioinformatics Institute (EBI)/Sanger
Institute,
• NCBI Analysis Pipeline,
• Oak Ridge National Laboratories (ORNL) Genome Channel.