Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER

Aggarwal, Gautam; Ramaswamy, Ramakrishna

doi:10.1007/bf02703679

Cited by 75 publications

(53 citation statements)

References 21 publications

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“…University of Minnesota (www.cbc.umn.edu), and transfer RNAs were predicted with TRNASCAN-SE (17)(18)(19)(20). Comparative genomic analysis was peformed with Mycobacterium tuberculosis (Mtb), strain H37Rv (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

The complete genome sequence ofMycobacterium aviumsubspeciesparatuberculosis

Bannantine

Zhang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

407

356

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We describe here the complete genome sequence of a common clone of Mycobacterium avium subspecies paratuberculosis (Map) strain K-10, the causative agent of Johne's disease in cattle and other ruminants. The K-10 genome is a single circular chromosome of 4,829,781 base pairs and encodes 4,350 predicted ORFs, 45 tRNAs, and one rRNA operon. In silico analysis identified >3,000 genes with homologs to the human pathogen, M. tuberculosis (Mtb), and 161 unique genomic regions that encode 39 previously unknown Map genes. Analysis of nucleotide substitution rates with Mtb homologs suggest overall strong selection for a vast majority of these shared mycobacterial genes, with only 68 ORFs with a synonymous to nonsynonymous substitution ratio of >2. Comparative sequence analysis reveals several noteworthy features of the K-10 genome including: a relative paucity of the PE͞PPE family of sequences that are implicated as virulence factors and known to be immunostimulatory during Mtb infection; truncation in the EntE domain of a salicyl-AMP ligase (MbtA), the first gene in the mycobactin biosynthesis gene cluster, providing a possible explanation for mycobactin dependence of Map; and Map-specific sequences that are likely to serve as potential targets for sensitive and specific molecular and immunologic diagnostic tests. Taken together, the availability of the complete genome sequence offers a foundation for the study of the genetic basis for virulence and physiology in Map and enables the development of new generations of diagnostic tests for bovine Johne's disease.

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Section: Methodsmentioning

confidence: 99%

The complete genome sequence ofMycobacterium aviumsubspeciesparatuberculosis

Bannantine

Zhang

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

407

356

View full text Add to dashboard Cite

show abstract

“…The existing numerical encoding method of Voss is the numerical representation [23] that maps the alphabets A, G, C and T into four-indicator sequences x A (n), x T (n), x C (n) and x G (n) substituting 1 for presence or 0 for absence of respective nucleotide. Another four-indicator sequence called relative frequency indicator sequence, based on various coding statistics like single-nucleotide, dinucleotide and trinucleotide biases was incorporated into the algorithm to improve the selectivity and sensitivity of filter methods [24,25]. The paired numeric [26] method deals with complementary property of nucleotides and assign +1 and -1 to show the presence of A-T and C-G nucleotide pairs respectively.…”

Section: Proposed Numerical Representationmentioning

confidence: 99%

Detection of Mutation-Hotspots and Exon-Deletions using Digital Signal Processing in Duchenne Muscular Dystrophy (DMD) Gene

Meher¹,

Rath²

2014

IOSRJDMS

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“…For prokaryotic genomes, these combined methods are highly successful, identifying over 95% of the genes (e.g. Aggarwal and Ramaswamy, 2002), although the exact determination of the start site location remains more problematic because of the absence of relatively strong sequence patterns. The process of predicting genes in higher eukaryotic genomes is complicated by several factors, including complex gene organization, the presence of large numbers of introns and repetitive elements, and the sheer size of the genomic sequence (for a review, see Zhang, 2002).…”

Section: Exploitation Of Evolutionary Concepts and Phylogenetic-basedmentioning

confidence: 99%

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

Levasseur¹,

Pontarotti²,

Poch

et al. 2008

Evol Bioinform Online

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The recent availability of the complete genome sequences of a large number of model organisms, together with the immense amount of data being produced by the new high-throughput technologies, means that we can now begin comparative analyses to understand the mechanisms involved in the evolution of the genome and their consequences in the study of biological systems. Phylogenetic approaches provide a unique conceptual framework for performing comparative analyses of all this data, for propagating information between different systems and for predicting or inferring new knowledge. As a result, phylogeny-based inference systems are now playing an increasingly important role in most areas of high throughput genomics, including studies of promoters (phylogenetic footprinting), interactomes (based on the presence and degree of conservation of interacting proteins), and in comparisons of transcriptomes or proteomes (phylogenetic proximity and co-regulation/co-expression). Here we review the recent developments aimed at making automatic, reliable phylogeny-based inference feasible in large-scale projects. We also discuss how evolutionary concepts and phylogeny-based inference strategies are now being exploited in order to understand the evolution and function of biological systems. Such advances will be fundamental for the success of the emerging disciplines of systems biology and synthetic biology, and will have wide-reaching effects in applied fields such as biotechnology, medicine and pharmacology.

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Ab initio gene identification: Prokaryote genome annotation with GeneScan and GLIMMER

Cited by 75 publications

References 21 publications

The complete genome sequence ofMycobacterium aviumsubspeciesparatuberculosis

The complete genome sequence ofMycobacterium aviumsubspeciesparatuberculosis

Detection of Mutation-Hotspots and Exon-Deletions using Digital Signal Processing in Duchenne Muscular Dystrophy (DMD) Gene

Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology

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