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Gene recognition in eukaryotic DNA by comparison of genomic sequences

P. S. Novichkov, M. S. Gelfand, A. A. Mironov
2001 Bioinformatics  
Motivation: Sequencing of complete eukaryotic genomes and large syntenic fragments of genomes makes it possible to apply genomic comparison for gene recognition.  ...  This is caused by a large amount of sequence conservation in non-coding regions of the human and mouse genes probably due to regulatory elements.  ...  This study was partially supported by grants from the Russian State Scientific Program 'Human Genome ', INTAS (99-1476), the Howard Hughes Medical Institute (55000309), and the Ludwig Institute for Cancer  ... 
doi:10.1093/bioinformatics/17.11.1011 pmid:11724729 fatcat:kvrap5zd2jd4bd7p3ywhcdqn7y

Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution

Yoshikazu Furuta, Ichizo Kobayashi
2012 Mobile Genetic Elements  
This work was supported by the Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (21370001 to I.K., 24790412 to Y.F.) and from the Ministry of Education, Culture  ...  , Sports, Science and Technology (MEXT) (24113506 to I.K., 24119503 to Y.F.); the Global COE Project of Genome Information Big Bang from MEXT to I.K.; Grant in Promotion of Basic Research Activities for  ...  Change in Sequence Specificity of DNA Methylation by Movement of Target Recognition Domains By comparison of RM systems in various strains of Helicobacter pylori, we found two novel mechanisms for movement  ... 
doi:10.4161/mge.23371 pmid:23481556 pmcid:PMC3575425 fatcat:qqtfo4arxff45pabnuibqbxpza

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors

A. A. Mironov, P. S. Novichkov, M. S. Gelfand
2001 Bioinformatics  
Resume Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors.  ...  A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts.  ...  This work was partially supported by Anchorgen, Inc. (http://www.anchorgen.com).  ... 
doi:10.1093/bioinformatics/17.1.13 pmid:11222258 fatcat:aafrewmzxred7m2v7vihpiaau4

Splice Site Recognition Using Lower Dimensional LHMM Features and SVM Classifier

Sejal Sahu
2017 International Journal for Research in Applied Science and Engineering Technology  
Recognition of coding region from DNA sequence has gained immense importance in the field of the research of gene identification.  ...  Splice sites which are the borders between exons and introns in DNA sequence are found in the eukaryotic organism.  ...  The main focus of human genome project was the identification of genes in eukaryotic genomes, but a still accurate number of genes in eukaryotic genomes are still unknown and research is going on.  ... 
doi:10.22214/ijraset.2017.11315 fatcat:o2kksdrvbfcebj6fyly5duuql4

United we stand: big roles for small RNA gene clusters

Brice Felden, Luc Paillard
2016 RNA: A publication of the RNA Society  
Unexpectedly and strikingly, bacterial and eukaryotic immunity RNA clusters share substantial functional and mechanistic resemblances in fighting nucleic acid intruders.  ...  Prokaryotes and eukaryotes evolved relatively similar RNA-based molecular mechanisms to fight potentially deleterious nucleic acids coming from phages, transposons, or viruses.  ...  Comparison showing the close resemblance of prokaryotic and eukaryotic immunity cluster RNA. Molecular defense against DNA intruders in the two domains was subdivided into nine distinct steps.  ... 
doi:10.1261/rna.058891.116 pmid:27881475 pmcid:PMC5238787 fatcat:n7xni47tjfbctbbom2rz772cwu

Gene Families: The Taxonomy of Protein Paralogs and Chimeras

S. Henikoff
1997 Science  
Ancient duplications and rearrangements of protein-coding segments have resulted in complex gene family relationships.  ...  As a result, gene products may acquire new specificities, altered recognition properties, or modified functions.  ...  This relationship was not detected by pairwise sequence comparisons, but rather by recognition of a tubulin motif in FtsZ.  ... 
doi:10.1126/science.278.5338.609 pmid:9381171 fatcat:2v6outpxfzftvaxl7zmksygjwa

Two Types of ftsZ Genes Isolated from the Unicellular Primitive Red Alga Galdieria sulphuraria

M. Takahara, H. Takahashi, S. Matsunaga, A. Sakai, S. Kawano, T. Kuroiwa
1999 Plant and Cell Physiology  
A comparison of the FtsZs of G. sulphuraria and other organisms shows that FtsZ is highly and universally conserved among prokaryotes, primitive eukaryotic algae, and higher plants.  ...  FtsZ plays a crucial role in bacterial cell division, and may be involved in plastid division in eukaryotes.  ...  This work was supported by a Grant for Special Promoted Research (project no. 06101002) to T.K. from the Ministry of Education, Science and Culture of Japan.  ... 
doi:10.1093/oxfordjournals.pcp.a029606 pmid:10555302 fatcat:r2ev3jifnffgro4ixkk35a2mxq

Did DNA replication evolve twice independently?

D. D. Leipe, L. Aravind, E. V. Koonin
1999 Nucleic Acids Research  
We performed detailed sequence comparisons of the proteins that fulfill indispensable functions in DNA replication and classified them into four main categories with respect to the conservation in bacteria  ...  Consequently, the moderntype system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.  ...  The recognition of homology between other replication proteins where sequence similarity was initially hard to detect has been made possible by structural comparisons.  ... 
doi:10.1093/nar/27.17.3389 pmid:10446225 pmcid:PMC148579 fatcat:jf7cl7xkxrdprmspgfk4ucpzwu

Expressing the human genome

Rossella Tupler, Giovanni Perini, Michael R. Green
2001 Nature  
A plethora of potential new factors are implicated by sequence in nuclear gene expression, revealing a substantial but selective increase in complexity compared with Drosophila melanogaster and Caenorhabditis  ...  We have searched the human genome for genes encoding new proteins that may be involved in three nuclear gene expression processes: transcription, pre-messenger RNA splicing and polyadenylation.  ...  Acknowledgements M.R.G. is an investigator of the Howard Hughes Medical Institute. This work was supported in part by a grant from NIH to M.R.G.  ... 
doi:10.1038/35057011 pmid:11237001 fatcat:eedampdfjjejrgcb6z7bted2ky

Functional Reassembly of Split Enzymes On-Site: A Novel Approach for Highly Sequence-Specific Targeted DNA Methylation

Antal Kiss, Elmar Weinhold
2008 ChemBioChem  
Keywords: DNA methylation · DNA recognition · gene silencing · protein fragment complementation · zinc finger proteins  ...  Acknowledgements Funding by the European Commission's Sixth Framework Program (COOP-CT-2005-017984) is gratefully acknowledged.  ...  [1] Recognition of the importance of DNA methylation in gene regulation raised the possibility of silencing selected genes by exogenous, targeted methylation of their promoters.  ... 
doi:10.1002/cbic.200700662 pmid:18189249 fatcat:u55wa5bwmjfzfpgtci7pkylqwe

Exaptation of Protein Coding Sequences from Transposable Elements [chapter]

N.J. Bowen, I.K. Jordan
2007 Genome Dynamics  
For instance, TEs can cause phenotypically relevant mutations by inserting in or around genes, and ectopic recombination, mediated by homologous element sequences dispersed throughout the genome, can lead  ...  One of the many ways that TEs contribute to the function and evolution of the genomes in which they reside is through the donation of host protein coding sequences (CDSs).  ...  Selfish DNA Theory of TEs The recognition of TEs' broad distribution and high copy numbers, i.e. their evolutionary success, in eukaryotic genomes posed an explanatory challenge to biologists.  ... 
doi:10.1159/000107609 pmid:18753790 fatcat:epzo4ndwg5evbdkfhfaladtdga

Promoter Prediction on a Genomic Scale---The Adh Experience

U. Ohler
2000 Genome Research  
We describe our statistical system for promoter recognition in genomic DNA with which we took part in the Genome Annotation Assessment Project (GASP1).  ...  We compare the results of both versions with each other and examine how well the application on a genomic scale compares with the results we previously obtained on smaller data sets.  ...  This compares well with the results described in the comparison of promoter recognition algorithms in vertebrate DNA (Fickett and Hatzigeorgiou 1997) , especially considering the smaller amount of available  ... 
doi:10.1101/gr.10.4.539 pmid:10779494 pmcid:PMC310866 fatcat:jjxobjji5vhxxfwoai2zsmk7ee

ROLE OF BIOINFORMATICS IN AGRICULTURE AND SUSTAINABLE DEVELOPMENT
English

SINGH VK, SINGH AK, CHAND R, KUSHWAHA C
2011 International Journal of Bioinformatics Research  
During the last two decades enormous data has been generated in biological science, firstly, with the onset of sequencing the genomes of model organisms and, secondly, rapid application of high throughput  ...  Introduction: the genomic era in 21 st century The genomic era has seen a massive explosion in the amount of biological information due to huge advances in the fields of molecular biology and genomics.  ...  In eukaryotes such as plants, protozoa and animals, however, 'genome' carries the typical connotation of only information on chromosomal DNA [9] .  ... 
doi:10.9735/0975-3087.3.2.221-226 fatcat:uokfvy447nenjc5op7i5r3f66y

Methylation of either cytosine in the recognition sequence CGCG inhibitsThaI cleavage of DNA

Jeannine S. Strobl, E.Brad Thompson
1984 Nucleic Acids Research  
Methylation of either cytosine in the ThaI recognition sequence rendered the DNA resistant to ThaI cleavage.  ...  We conclude that ThaI is a useful restriction enzyme for the analysis of mC at CGCG sequences in eukaryotic DNA.  ...  John Baxter for providing the GH cDNA clone used in these studies. This work was supported in part by a Pharmaceutical Manufacturers Association Research Starter Grant.  ... 
doi:10.1093/nar/12.21.8073 pmid:6209609 pmcid:PMC320278 fatcat:nebkr4rcfzcq3knwptyszsu66y

Integrated databases and computer systems for studying eukaryotic gene expression

N. A. Kolchanov, M. P. Ponomarenko, A. S. Frolov, E. A. Ananko, F. A. Kolpakov, E. V. Ignatieva, O. A. Podkolodnaya, T. N. Goryachkovskaya, I. L. Stepanenko, T. I. Merkulova, V. V. Babenko, Y. V. Ponomarenko (+10 others)
1999 Bioinformatics  
knowledge that can be further used for analysis of regulatory genomic sequences.  ...  ) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins.  ...  the Russian Human Genome Program, the Ministry of Science and Technology of Russian Federation, Integrated Program of Siberian Department of Russian Academy of Sciences.  ... 
doi:10.1093/bioinformatics/15.7.669 pmid:10487874 fatcat:v53hphh7v5cjhctnlixpxingyy
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