A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

Suckow, Jörg Michael; Amano, Naoki; Ohfuku, Yuko; Kakinuma, Jun; Koike, Hideaki; Suzuki, Masashi

doi:10.1016/s0014-5793(98)00323-8

Cited by 12 publications

(4 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For initiation of transcription, TATA-binding protein and transcription factor B are required. The transcription signals identified upstream of putative genes in Pyrococcus OT3 (OGT of 98°C) were closer to AAAATTTATAAA (16), whereas those identified in T. volcanium in this study were closer to AAAATTTATATA. The consensus sequence of Pyrococcus OT3 has a higher equilibrium binding constant to TATA-binding protein, as the consensus sequence of T. volcanium has a higher Each column is composed of 750 lines from top to bottom, and each line is an assembly of 105 microsquares from left to right.…”

Section: Methodscontrasting

confidence: 41%

“…1 A and C, gene-coding regions can be visualized as stripes in red and black, where regions are coding for genes along the strand of the sequence shown, or stripes in yellow and white, where regions are coding for genes along the complementary strand. These stripes are created because in gene-coding regions purines are more frequent than pyrimidines as a consequence of the triplet periodic combination (16,29). The average number of bases in genes is approximately 1,000; thus, in Fig.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

Kawashima

Amano

Koike

et al. 2000

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

Self Cite

180

View full text Add to dashboard Cite

The complete genomic sequence of the archaeon Thermoplasma volcanium, possessing optimum growth temperature (OGT) of 60°C, is reported. By systematically comparing this genomic sequence with the other known genomic sequences of archaea, all possessing higher OGT, a number of strong correlations have been identified between characteristics of genomic organization and the OGT. With increasing OGT, in the genomic DNA, frequency of clustering purines and pyrimidines into separate dinucleotides rises (e.g., by often forming AA and TT, whereas avoiding TA and AT). Proteins coded in a genome are divided into two distinct subpopulations possessing isoelectric points in different ranges (i.e., acidic and basic), and with increasing OGT the size of the basic subpopulation becomes larger. At the metabolic level, genes coding for enzymes mediating pathways for synthesizing some coenzymes, such as heme, start missing. These findings provide insights into the design of individual genomic components, as well as principles for coordinating changes in these designs for the adaptation to new environments.

show abstract

Section: Methodscontrasting

confidence: 41%

Section: Resultsmentioning

confidence: 99%

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

Kawashima

Amano

Koike

et al. 2000

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

Self Cite

180

View full text Add to dashboard Cite

show abstract

“…Preliminary work shows that alignment of multiple codons within one gene also shows periodicity. This agrees with work done for some genes in Pyrococcus [13]. There has been some suggestion that examination of periodicity within ORFs could assist in gene identification [14].…”

Section: Resultssupporting

confidence: 88%

Visualization of aligned genomic open reading frame data*

Boyle

2003

Biochem Molecular Bio Educ

View full text Add to dashboard Cite

Students can better appreciate the value of genomic data if they are asked to use the data themselves. However, in general the enormous volume of data involved makes detailed examination difficult. Here we present a web site that allows students to study one particular aspect of sequenced genomes. They are able to align the open reading frames (ORFs) of any available genome that is of reasonable size. The ORFs may be aligned using either the start codon or the stop codon as the starting points. Results will readily show the presence of common ribosome binding sites as well as reveal interesting order within the ORFs that is nonexistent outside of them. Students will be able to ask various questions involving comparisons of genomes and see the results presented in both a tabular and graphic format. An example problem is presented under "Results."Keywords: Alignment, visualization, genomes, ORF.The past few years have seen an explosion of DNA sequencing results. In particular, entire genomes, both prokaryotic and eukaryotic, are now available for study due to rapid advances in sequencing methodologies. The first viral sequence, phi-X174, was published in 1977 and consisted of 5386 bases in a single-stranded genome [1]. The first eubacterial sequence, Haemophilus influenzae, was completed in 1995 and was 1,830,137 base pairs long [2]. Yeast and human draft sequence lengths testify to the power of the available methods and the quantity of information produced. However, the enormous size of even the simplest genomes sometimes hinders easy use of the available data.Students are presented with information relating to cis elements affecting transcription and translation by several different methods. The most common is a simple presentation of "consensus" data. For a more detailed appreciation, they are given tables of aligned sequences of these elements. Recent statistical approaches have provided a more accurate way to present summaries of the data. Two related methods are based on a maximum likelihood statistic. One involves a weight matrix [3], and the other involves an information theory approach [4]. Both methods have their proponents and virtues [5,6]. A typical output shows cis sites in terms of varying sizes of base logos (see Ref. 7 for example).Here we present an alternate way to display and examine alignable sequence data. We take advantage of the availability of genomic data to show that open reading frames (ORFs) 1 from entire genomes can be aligned to reveal global patterns in DNA data. We present a web site where students can ask their own questions about sequences and produce the results quickly.

show abstract

“…On the other hand, it is well known that there are many pseudogenes in intergenic regions of prokaryotic and eukaryotic DNA sequences. [27][28][29] Harrison et al 28 have analyzed pseudogenes in the worm and found that there is about one pseudogene for every eight genes. Pseudogenes also exist in each human chromosome.…”

Section: Frame Independence Of the Algorithmmentioning

confidence: 99%

Recognizing shorter coding regions of human genes based on the statistics of stop codons

2002

View full text Add to dashboard Cite

With the quick progress of the Human Genome Project, a great amount of uncharacterized DNA sequences needs to be annotated copiously by better algorithms. Recognizing shorter coding sequences of human genes is one of the most important problems in gene recognition, which is not yet completely solved. This paper is devoted to solving the issue using a new method. The distributions of the three stop codons, i.e., TAA, TAG and TGA, in three phases along coding, noncoding, and intergenic sequences are studied in detail. Using the obtained distributions and other coding measures, a new algorithm for the recognition of shorter coding sequences of human genes is developed. The accuracy of the algorithm is tested based on a larger database of human genes. It is found that the average accuracy achieved is as high as 92.1% for the sequences with length of 192 base pairs, which is confirmed by sixfold cross-validation tests. It is hoped that by incorporating the present method with some existing algorithms, the accuracy for identifying human genes from unannotated sequences would be increased.

show abstract

A transcription frame‐based analysis of the genomic DNA sequence of a hyper‐thermophilic archaeon for the identification of genes, pseudo‐genes and operon structures

Cited by 12 publications

References 35 publications

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium

Visualization of aligned genomic open reading frame data*

Recognizing shorter coding regions of human genes based on the statistics of stop codons

Contact Info

Product

Resources

About