In
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to
find genes in prokaryotic
DNA.
"It is effective at finding genes in
bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
,
archea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaeb ...
,
viruses
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsky's 1 ...
, typically finding 98-99% of all relatively long
protein coding genes".
GLIMMER was the first system that used the
interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by
Steven Salzberg
Steven Lloyd Salzberg (born 1960) is an American computational biologist and computer scientist who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at Johns Hopkins University, where he is als ...
, Art Delcher, and their colleagues at the ''Center for Computational Biology'' at
Johns Hopkins University
Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private university, private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hem ...
. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with
Owen White
Owen White is a bioinformatician and director of the Institute For Genome Sciences at the University of Maryland School of Medicine. He is known for his work on the bioinformatics tools GLIMMER and MUMmer.
Education
White studied biotechnology a ...
.
Versions
GLIMMER 1.0
First Version of GLIMMER "i.e., GLIMMER 1.0" was released in 1998 and it was published in the paper ''Microbial gene identification using interpolated Markov model''.
Markov models were used to identify microbial genes in GLIMMER 1.0. GLIMMER considers the local composition sequence dependencies which makes GLIMMER more flexible and more powerful when compared to fixed-order
Markov model.
There was a comparison made between
interpolated Markov model used by GLIMMER and fifth order Markov model in the paper ''Microbial gene identification using interpolated Markov models''.
"GLIMMER algorithm found 1680 genes out of 1717 annotated genes in
Haemophilus influenzae
''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacteria ...
where fifth order
Markov model found 1574 genes. GLIMMER found 209 additional genes which were not included in 1717 annotated genes where fifth order
Markov model found 104 genes."'
GLIMMER 2.0
Second Version of GLIMMER i.e., GLIMMER 2.0 was released in 1999 and it was published in the paper ''Improved microbial identification with GLIMMER''.
This paper
provides significant technical improvements such as using interpolated context model instead of interpolated Markov model and resolving overlapping genes which improves the accuracy of GLIMMER.
Interpolated context models are used instead of
interpolated Markov model which gives the flexibility to select any base. In interpolated Markov model probability distribution of a base is determined from the immediate preceding bases. If the immediate preceding base is irrelevant
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
translation, interpolated Markov model still considers the preceding base to determine the probability of given base where as interpolated context model which was used in GLIMMER 2.0 can ignore irrelevant bases. False positive predictions were increased in GLIMMER 2.0 to reduce the number of false negative predictions. Overlapped genes are also resolved in GLIMMER 2.0.
Various comparisons between GLIMMER 1.0 and GLIMMER 2.0 were made in the paper ''Improved microbial identification with GLIMMER''
which shows improvement in the later version. "Sensitivity of GLIMMER 1.0 ranges from 98.4 to 99.7% with an average of 99.1% where as GLIMMER 2.0 has a sensitivity range from 98.6 to 99.8% with an average of 99.3%. GLIMMER 2.0 is very effective in finding genes of high density. The parasite
Trypanosoma brucei
''Trypanosoma brucei'' is a species of parasitic Kinetoplastida, kinetoplastid belonging to the genus ''Trypanosoma'' that is present in sub-Saharan Africa. Unlike other protozoan parasites that normally infect blood and tissue cells, it is exclus ...
, responsible for causing
African sleeping sickness
African trypanosomiasis, also known as African sleeping sickness or simply sleeping sickness, is an insect-borne parasitic infection of humans and other animals. It is caused by the species '' Trypanosoma brucei''. Humans are infected by two ty ...
is being identified by GLIMMER 2.0"
GLIMMER 3.0
Third version of GLIMMER, "GLIMMER 3.0" was released in 2007 and it was published in the paper ''Identifying bacterial genes and endosymbiont DNA with Glimmer''.
This paper describes several major changes made to the GLIMMER system including improved methods to identify coding regions and start
codon
The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...
. Scoring of ORF in GLIMMER 3.0 is done in reverse order i.e., starting from stop codon and moves back towards the start codon. Reverse scanning helps in identifying the coding portion of the gene more accurately which is contained in the context window of IMM. GLIMMER 3.0 also improves the generated training set data by comparing the long-ORF with universal amino acid distribution of widely disparate bacterial genomes."GLIMMER 3.0 has an average long-ORF output of 57% for various organisms where as GLIMMER 2.0 has an average long-ORF output of 39%."
GLIMMER 3.0 reduces the rate of false positive predictions which were increased in GLIMMER 2.0 to reduce the number of false negative predictions. "GLIMMER 3.0 has a start-site prediction accuracy of 99.5% for 3'5' matches where as GLIMMER 2.0 has 99.1% for 3'5' matches. GLIMMER 3.0 uses a new algorithm for scanning coding regions, a new start site detection module, and architecture which integrates all gene predictions across an entire genome."
Minimum description length
Theoretical and Biological Foundation
The GLIMMER project helped introduce and popularize the use of variable length models in Computational Biology and Bioinformatics that subsequently have been applied to numerous problems such as protein classification and others. Variable length modeling was originally pioneered by information theorists and subsequently ingeniously applied and popularized in data compression (e.g. Ziv-Lempel compression). Prediction and compression are intimately linked using
Minimum Description Length Principles. The basic idea is to create a dictionary of frequent words (motifs in biological sequences). The intuition is that the frequently occurring motifs are likely to be most predictive and informative. In GLIMMER the interpolated model is a mixture model of the probabilities of these relatively common motifs. Similarly to the development of HMMs in Computational Biology, the authors of GLIMMER were conceptually influenced by the previous application of another variant of interpolated Markov models to speech recognition by researchers such as Fred Jelinek (IBM) and Eric Ristad (Princeton). The learning algorithm in GLIMMER is different from these earlier approaches.
Access
GLIMMER can be downloaded fro
The Glimmer home page (requires a C++
compiler
In computing, a compiler is a computer program that translates computer code written in one programming language (the ''source'' language) into another language (the ''target'' language). The name "compiler" is primarily used for programs that ...
).
Alternatively, an online version is hosted by
NCBI
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 (NIH). It is approved and funded by the government of the United States. The ...
br>
How it works
# GLIMMER primarily searches for long-
open reading frame, ORFS. An open reading frame might overlap with any other open reading frame which will be resolved using the technique described in the sub section. Using these long-ORFS and following certain amino acid distribution GLIMMER generates
training set
In machine learning, a common task is the study and construction of algorithms that can learn from and make predictions on data. Such algorithms function by making data-driven predictions or decisions, through building a mathematical model from ...
data.
# Using these training data, GLIMMER trains all the six Markov models of coding DNA from zero to eight order and also train the model for
noncoding DNA
# GLIMMER tries to calculate the probabilities from the data. Based on the number of observations, GLIMMER determines whether to use fixed order
Markov model or
interpolated Markov model.
## If the number of observations are greater than 400, GLIMMER uses fixed order Markov model to obtain there probabilities.
## If the number of observations are less than 400, GLIMMER uses
interpolated Markov model which is briefly explained in the next sub section.
# GLIMMER obtains score for every long-ORF generated using all the six coding DNA models and also using non-coding DNA model.
# If the score obtained in the previous step is greater than a certain threshold then GLIMMER predicts it to be a gene.
The steps explained above describes the basic functionality of GLIMMER. There are various improvements made to GLIMMER and some of them are described in the following sub-sections.
The GLIMMER system
GLIMMER system consists of two programs. First program called build-imm, which takes an input set of sequences and outputs the
interpolated Markov model as follows.
The probability for each base i.e., A,C,G,T for all
k-mers for 0 ≤ k ≤ 8 is computed. Then, for each
k-mer, GLIMMER computes weight. New sequence probability is computed as follows.
where n is the length of the sequence
is the
oligomer
In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relativ ...
at position x.
, the
-order
interpolated Markov model score is computed as
"where
is the weight of the
k-mer at position x-1 in the sequence S and
is the estimate obtained from the training data of the probability of the base located at position x in the
-order model."
The probability of base
given the i previous bases is computed as follows.
"The value of
associated with
can be regarded as a measure of confidence in the accuracy of this value as an estimate of the true probability. GLIMMER uses two criteria to determine
. The first of these is simple frequency occurrence in which the number of occurrences of context string
in the training data exceeds a specific threshold value, then
is set to 1.0. The current default value for threshold is 400, which gives 95% confidence. When there are insufficient sample occurrences of a context string, build-imm employ additional criteria to determine
value. For a given context string
of length i, build-imm compare the observed frequencies of the following base
,
,
,
with the previously calculated
interpolated Markov model probabilities using the next shorter context,
,
,
,
. Using a
test, build-imm determine how likely it is that the four observed frequencies are consistent with the IMM values from the next shorter context."
The second program called glimmer, then uses this IMM to identify putative gene in an entire genome. GLIMMER identifies all the
open reading frame
In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readin ...
which score higher than threshold and check for overlapping genes. Resolving overlapping genes is explained in the next sub-section.
Equations and explanation of the terms used above are taken from the paper 'Microbial gene identification using interpolated Markov models''
''
Resolving overlapping genes
In GLIMMER 1.0, when two genes A and B overlap, the overlap region is scored. If A is longer than B, and if A scores higher on the overlap region, and if moving B's start site will not resolve the overlap, then B is rejected.
GLIMMER 2.0 provided a better solution to resolve the overlap. In GLIMMER 2.0, when two potential genes A and B overlap, the overlap region is scored. Suppose gene A scores higher, four different orientations are considered.
![Case 1](https://upload.wikimedia.org/wikipedia/commons/1/1c/Case_1.png)
In the above case, moving of start sites does not remove the overlap. If A is significantly longer than B, then B is rejected or else both A and B are called genes, with a doubtful overlap.
![Case2](https://upload.wikimedia.org/wikipedia/commons/f/f2/Case2.png)
In the above case, moving of B can resolve the overlap, A and B can be called non overlapped genes but if B is significantly shorter than A, then B is rejected.
![Case3](https://upload.wikimedia.org/wikipedia/commons/6/65/Case3.png)
In the above case, moving of A can resolve the overlap. A is only moved if overlap is a small fraction of A or else B is rejected.
![Case4](https://upload.wikimedia.org/wikipedia/commons/7/76/Case4.png)
In the above case, both A and B can be moved. We first move the start of B until the overlap region scores higher for B. Then we move the start of A until it scores higher. Then B again, and so on, until either the overlap is eliminated or no further moves can be made.
The above example has been taken from the paper 'Identifying bacterial genes and endosymbiont DNA with Glimmer'
Ribosome binding sites
Ribosome binding site A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers t ...
(RBS) signal can be used to find true start site position. GLIMMER results are passed as an input for RBSfinder program to predict ribosome binding sites. GLIMMER 3.0 integrates RBSfinder program into gene predicting function itself.
ELPH software( which was determined as highly effective at identifying RBS in the paper
) is used for identifying RBS and is available at thi
website Gibbs sampling
In statistics, Gibbs sampling or a Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm for obtaining a sequence of observations which are approximated from a specified multivariate probability distribution, when direct sampling is dif ...
algorithm is used to identify shared
motif
Motif may refer to:
General concepts
* Motif (chess composition), an element of a move in the consideration of its purpose
* Motif (folkloristics), a recurring element that creates recognizable patterns in folklore and folk-art traditions
* Moti ...
in any set of sequences. This shared
motif
Motif may refer to:
General concepts
* Motif (chess composition), an element of a move in the consideration of its purpose
* Motif (folkloristics), a recurring element that creates recognizable patterns in folklore and folk-art traditions
* Moti ...
sequences and their length is given as input to ELPH. ELPH then computes the position weight matrix(PWM) which will be used by GLIMMER 3 to score any potential RBS found by RBSfinder. The above process is done when we have a substantial amount of training genes. If there are inadequate number of training genes, GLIMMER 3 can bootstrap itself to generate a set of gene predictions which can be used as input to ELPH. ELPH now computes PWM and this PWM can be again used on the same set of genes to get more accurate results for start-sites. This process can be repeated for many iterations to obtain more consistent PWM and gene prediction results.
Performance
Glimmer supports genome annotation efforts on a wide range of bacterial, archaeal, and viral species. In a large-scale reannotation effort at the DNA Data Bank of Japan (DDBJ, which mirrors
Genbank). Kosuge ''et al.'' (2006)
examined the gene finding methods used for 183 genomes. They reported that of these projects, Glimmer was the gene finder for 49%, followed by
GeneMark
GeneMark is a generic name for a family of ab initio gene prediction programs developed at the Georgia Institute of Technology in Atlanta. Developed in 1993, original GeneMark was used in 1995 as a primary gene prediction tool for annotation of ...
with 12%, with other algorithms used in 3% or fewer of the projects. (They also reported that 33% of genomes used "other" programs, which in many cases meant that they could not identify the method. Excluding those cases, Glimmer was used for 73% of the genomes for which the methods could be unambiguously identified.) Glimmer was used by the DDBJ to re-annotate all bacterial genomes in the International Nucleotide Sequence Databases.
It is also being used by this group to annotate viruses.
Glimmer is part of the bacterial annotation pipeline at the National Center for Biotechnology Information (NCBI), which also maintains a web server for Glimmer, as do sites in Germany, Canada,.
According to Google Scholar, as of early 2011 the original Glimmer article (Salzberg et al., 1998)
has been cited 581 times, and the Glimmer 2.0 article (Delcher et al., 1999)
has been cited 950 times.
References
{{reflist
External links
The Glimmer home page at CCB, Johns Hopkins University from which the software can be downloaded.
Bioinformatics
Markov models