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P: probability of exons
S
predict genes in a variety of eukaryotic organisms,
including plants, , animals, and fungi.
Evidence Source for Prediction:
Introduction
used in 1995 as a primary gene prediction
tool for annotation of the first completely
sequenced bacterial genome of
Haemophilus influenzae
Algorithms
Core Algorithm:
Additional Algorithms:
• Inhomogeneous Three Periodic Markov Chain Models: These models capture the specific
patterns of nucleotides within coding regions.
• Homogeneous Three Periodic Markov Chain Models:
These models identify non-coding regions
• Bayesian approach:
It is used to gene prediction in two DNA strands simultaneously
• Ribosome Binding Site (RBS) Model:
This model helps predict the start of genes in prokaryotic genomes by identifying the RBS
sequence upstream of the start codon.
• Heuristic Models:
These models estimate species-specific parameters for gene prediction in situations where
large genomic context is unavailable, such as viral genomes and metagenomic sequences.
• Self-training:
This technique allows the algorithm to automatically improve its parameter estimates by
iteratively predicting genes and using the predictions to further refine the model.
GeneMark Family of Gene Prediction Programs
Bacteria and Archaea:
GeneMark
GeneMark.hmm algorithm
GeneMarkS
GeneMarkS-2
Metagenomes and Metatranscriptomes:
MetaGeneMark
GeneMarkS-T
Eukaryotes:
GeneMark
GeneMark.hmm
GeneMark-ES
GeneMark-ET
GeneMark-EP+
GeneMark-ETP
Viruses
Heuristic models (MetaGeneMark and geneMarkS)
Eukaryotic genome annotation pipelines:
BRAKER1:
pipeline that combines AUGUDTUS with Genemark
-- uses GeneMark-ET and AUGUSTUS
BRAKER2:
integrates known proteins
-- uses GeneMark-EP+ and AUGUSTUS
BRAKER3:
integrates RNA-seq reads and known proteins
-- uses GeneMark-EP+ and AUGUSTUS
HOMEPAGE
LST (Locus Structure Table)
GFF (General Feature
Format)
GFF (General Feature
LST (Locus Structure Table)
Format)
• Focus: Primarily emphasizes the coding • Focus: Provides a more comprehensive view of the gene
potential of the sequence. structure, including exons, introns, coding regions etc
• Structure: Each line represents a coding • Structure: Each line represents a feature, with columns
region (CDS) or non-coding region (NCR), specifying:
with columns specifying: • Feature type: e.g., gene, exon, intron &untranslated region
• Strand: + or - indicating the DNA strand • Source: Program that predicted the feature.
coding direction. • Start and end positions
• Start and end position • Score: Optional value indicating the confidence in the
• Length: Size of the region in base pairs. prediction.
• Coding potential score: A numerical value • Strand: + or - indicating the DNA strand coding direction.
between 0 and 1, where 0 represents non- • Frame: For coding regions, indicates the reading frame.
coding and 1 indicates high coding • Attributes: Additional information about the feature, such
potential. as gene ID, protein ID, and specific gene name.
OUTPUT (LST format)
GFF Format
seq name Source Feature type Start & End position Confi. Strand Frame Attributes
PDF FILE OUTPUT
Window Length and Step:
These parameters define the size and spacing of
segments scanned by GeneMark while searching
for coding regions.
Threshold Value:
This value represents the minimum score required
for a region to be considered a potential coding
sequence.
PostScript graph:
This option indicates that the output includes a
graphical representation of the predictions.
Matrix:
It refers to a mathematical model that helps the
software determine the coding potential of a DNA
sequence
Order
This specifies the order of the Markov model used
in the matrix. A higher order model leads to more
accurate predictions.
The horizontal axis represents the
nucleotide position in the sequence, while
the vertical axis indicates the coding
potential score.
A score of 0.5 or higher is generally
considered to be indicative of a coding
region.
There is a long ORF spanning from
approximately 400 to 1600 bp with a
high coding potential score. This ORF is
likely to correspond to the actin protein-
coding sequence.
There are also a few shorter ORFs with
lower coding potential scores.
The region of the genome from
approximately 1200 to 2000 bp has a
relatively low coding potential score.
This may indicate that it contains non-
coding sequences, such as regulatory
elements or introns.
FGENESH: Ab Initio Gene
Prediction Tool
Introductio FGENESH (Flexible Gene Prediction
System) is an ab initio gene prediction tool
for prokaryotic and eukaryotic genomes.
n Algorithm:
It utilizes a hidden Markov model (HMM)
to scan DNA sequences and identify
potential coding regions, specifically exons
and introns.
Different
FGENESH-M - Prediction of multiple variants potential
genes in genomic DNA