Nicolas Carels and Diego Frias
Presentation
Outline:
Carels, N. and Frias, D. (2009). Classifying coding DNA with nucleotide statistics. Bioinformatics and Biology Insights 3:141-154. pdf.
1. Importance of accurate methods for the detection of coding DNA
Methods of Gene Detection
Extrinsic Methods
What is CDS?
The coding sequence (CDS) region of a gene is a sequence of nucleotides which corresponds to a sequence of amino acids in a protein,a typical CDS starts with ATG and ends in a stop codon (1).
http://www.google.ca/imghp?hl=en&tab=ii
Importance
A large amount of a DNA sequence is non-coding and identification of the coding regions is critical is determining the areas within the genome which code for certain proteins. Due to the advances in sequencing technologies there is large amount genomic data that needs to be searched to identify genes. This has created the demand for automated programs which can accurately and quickly identify the coding regions thereby providing insight into the function of a gene.
2. Methods for CDS Identification
A. Codon Usage
Hidden Markov Methods
Average Mutual Information and Spectral Rotation Measure
Carels, N. and Frias, D. (2009). Classifying coding DNA with nucleotide statistics. Bioinformatics and Biology Insights 3:141-154. pdf.
- Importance of accurate methods for the detection of coding DNA
- Methods which have been used to identify CDS
- Based on codon usage (Hidden Markov Models)
- Nucleotide periodicity
- Detection of ancestral codon ,RNY pattern
- Methodology behind UFM
- Results
- Discussion
- Scoring Purine Bias with UFM
- Comparison of CSF and UFM
- Comparison of the Classification of Coding and Non-coding ORF
by UFM
- References
1. Importance of accurate methods for the detection of coding DNA
Methods of Gene Detection
Extrinsic Methods
- search sequences for documented protein families (homology search)
- dependence on accurate input sequences, may miss proteins due
to low conservation of enzyme regions
- search sequence for patterns
- identification of CDS, introns, 5' and 3' gene extremities, and
gene structure
What is CDS?
The coding sequence (CDS) region of a gene is a sequence of nucleotides which corresponds to a sequence of amino acids in a protein,a typical CDS starts with ATG and ends in a stop codon (1).
http://www.google.ca/imghp?hl=en&tab=ii
Importance
A large amount of a DNA sequence is non-coding and identification of the coding regions is critical is determining the areas within the genome which code for certain proteins. Due to the advances in sequencing technologies there is large amount genomic data that needs to be searched to identify genes. This has created the demand for automated programs which can accurately and quickly identify the coding regions thereby providing insight into the function of a gene.
2. Methods for CDS Identification
A. Codon Usage
Hidden Markov Methods
- integration of information about the gene structure
- accuracy depends upon the training data being a good representative
Average Mutual Information and Spectral Rotation Measure
- independent of biological species
- tolerant to codon usage
- based on neucleotide statistics
- not very sensitive for CDS regions below 400bp
- greater success with CDS regions below 350bp
- based on nucleotide statistics
- measures codon asymmetry in 3 reading frames
- maximizes a function, set threshold determines the sequence classification (coding or not)
- independent of codon usage
- able to classify the coding frame among six possible frames of a ORF without parameter adjustment