The Experts below are selected from a list of 297 Experts worldwide ranked by ideXlab platform
Insuk Sohn - One of the best experts on this subject based on the ideXlab platform.
-
ICNC (2) - Exon Structure analysis via PCA and ICA of short-time fourier transform
Lecture Notes in Computer Science, 2005Co-Authors: Changha Hwang, David Chiu, Insuk SohnAbstract:We use principal component analysis (PCA) to identify Exons of a gene and further analyze their internal Structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the Exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the Exon and intron regions clearly. The codon based PCA reveals a weak internal Structure in some Exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the Exon and intron regions for this data. We hypothesize the existence of complex Exon Structures that deserve more detailed analysis.
-
Analyzing Exon Structure with PCA and ICA of Short-Time Fourier Transform
2004Co-Authors: Changha Hwang, Insuk SohnAbstract:We use principal component analysis (PCA) to identify Exons of a gene and further analyze their internal Structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the Exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the Exon and intron regions clearly. The codon based PCA reveals a weak internal Structure in some Exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the Exon and intron regions for this data. We hypothesize the existence of complex Exon Structures that deserve more detailed analysis.
Libor Grubhoffer - One of the best experts on this subject based on the ideXlab platform.
-
gene organization of a novel defensin of ixodes ricinus first annotation of an intron Exon Structure in a hard tick defensin gene and first evidence of the occurrence of two isoforms of one member of the arthropod defensin family
Insect Molecular Biology, 2007Co-Authors: Nataliia Rudenko, Marina Golovchenko, Libor GrubhofferAbstract:Antimicrobial peptides (defensins) are effectors of the immune system. Herein, we describe a novel Ixodes ricinus defensin gene(s), analyse its Structure and compare it with other known antimicrobial peptides from different tick species. For the first time, an intron/Exon Structure is discovered in a hard-tick defensin gene. The intron/Exon genomic organization of the gene is similar to the organization in Ornithodoros moubata, but not to that of the intronless defensins of Dermacentor variabilis and Ixodes scapularis. The analysis of the deduced amino acid sequences of different recombinants from the I. ricinus cDNA library reveals the presence of two defensin isoforms with three amino acid substitutions. Whether or not these substitutions affect the biological properties of the peptides is currently unknown. The expression of the defensin gene is strongly induced in the tick midgut after infection with Borrelia burgdorferi.
-
Gene organization of a novel defensin of Ixodes ricinus: first annotation of an intron/Exon Structure in a hard tick defensin gene and first evidence of the occurrence of two isoforms of one member of the arthropod defensin family
Insect molecular biology, 2007Co-Authors: Nataliia Rudenko, Marina Golovchenko, Libor GrubhofferAbstract:Antimicrobial peptides (defensins) are effectors of the immune system. Herein, we describe a novel Ixodes ricinus defensin gene(s), analyse its Structure and compare it with other known antimicrobial peptides from different tick species. For the first time, an intron/Exon Structure is discovered in a hard-tick defensin gene. The intron/Exon genomic organization of the gene is similar to the organization in Ornithodoros moubata, but not to that of the intronless defensins of Dermacentor variabilis and Ixodes scapularis. The analysis of the deduced amino acid sequences of different recombinants from the I. ricinus cDNA library reveals the presence of two defensin isoforms with three amino acid substitutions. Whether or not these substitutions affect the biological properties of the peptides is currently unknown. The expression of the defensin gene is strongly induced in the tick midgut after infection with Borrelia burgdorferi.
Vladimir A Ivanisenko - One of the best experts on this subject based on the ideXlab platform.
-
SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes.
Journal of bioinformatics and computational biology, 2017Co-Authors: Irina Medvedeva, Pavel S Demenkov, Vladimir A IvanisenkoAbstract:Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the Exons in genes. The study of the correlation between a site Structure and Exon Structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of Exon Structure of genes and primary and tertiary Structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped Exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D Structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the Exon Structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through Exon Structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/.
-
Computer analysis of protein functional sites projection on Exon Structure of genes in Metazoa
BMC Genomics, 2015Co-Authors: Irina V Medvedeva, Pavel S Demenkov, Vladimir A IvanisenkoAbstract:Background Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in Structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of Exon-intron Structure of the coding gene is still an actual problem. Results One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the Exon boundaries to the gene Structure. In this paper, we examined the discontinuity of the functional sites in the Exon-intron Structure of genes and the distribution of lengths and phases of the functional site encoding Exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same Exons, or in close Exons. The observed tendency to cluster the Exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the Structure of the Exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in Exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the Exon shuffling. Conclusions These results characterize the features of the coding Exon-intron Structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.
-
Computer analysis of protein functional sites projection on Exon Structure of genes in Metazoa.
BMC genomics, 2015Co-Authors: Irina V Medvedeva, Pavel S Demenkov, Vladimir A IvanisenkoAbstract:Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in Structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of Exon-intron Structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the Exon boundaries to the gene Structure. In this paper, we examined the discontinuity of the functional sites in the Exon-intron Structure of genes and the distribution of lengths and phases of the functional site encoding Exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same Exons, or in close Exons. The observed tendency to cluster the Exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the Structure of the Exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in Exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the Exon shuffling. These results characterize the features of the coding Exon-intron Structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.
-
Computer analysis of protein functional sites projection on Exon Structure of genes in Metazoa
BMC Genomics, 2015Co-Authors: Irina V Medvedeva, Pavel S Demenkov, Vladimir A IvanisenkoAbstract:Background Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in Structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of Exon-intron Structure of the coding gene is still an actual problem.
-
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes
Nucleic Acids Research, 2011Co-Authors: Irina V Medvedeva, Pavel S Demenkov, Nikolay A. Kolchanov, Vladimir A IvanisenkoAbstract:Search of interrelationships between the structural–functional protein organization and Exon Structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation of the Exon–intron Structure of the gene to the protein functional sites has been little studied. Development of resources containing data on projections of protein functional sites on eukaryotic genes is needed. We have developed SitEx, a database that contains information on functional site amino acid positions in the Exon Structure of encoding gene. SitEx is integrated with the BLAST and 3DExonScan programs. BLAST is used for searching sequence similarity between the query protein and polypeptides encoded by single Exons stored in SitEx. The 3DExonScan program is used for searching for structural similarity of the given protein with these polypeptides using superimpositions. The developed computer system allows users to analyze the coding features of functional sites by taking into account the Exon Structure of the gene, to detect the Exons involved in shuffling in protein evolution, also to design protein-engineering experiments. SitEx is accessible at http://www-bionet.sscc.ru/sitex/. Currently, it contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.
Michael Hiller - One of the best experts on this subject based on the ideXlab platform.
-
Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation.
Methods in molecular biology (Clifton N.J.), 2019Co-Authors: Virag Sharma, Michael HillerAbstract:Alignment-based gene identification methods utilize sequence conservation between orthologous protein-coding genes to annotate genes in newly sequenced genomes. CESAR is an approach that makes use of existing genome alignments to transfer genes from one genome to other aligned genomes, and thus generates comparative gene annotations. To accurately detect conserved Exons that exhibit an intact reading frame and consensus splice sites, CESAR produces a new alignment between orthologous Exons, taking information about the Exon's reading frame and splice site positions into account. Furthermore, CESAR is able to detect most evolutionary splice site shifts, which helps to annotate Exon boundaries at high precision. Here, we describe how to apply CESAR to generate comparative gene annotations for one or many species, and discuss the strengths and limitations of this approach. CESAR is available at https://github.com/hillerlab/CESAR2.0 .
-
Coding Exon-Structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.
Nucleic acids research, 2016Co-Authors: Virag Sharma, Anas Elghafari, Michael HillerAbstract:Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding Exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in Exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding Exons, while considering reading frame and splice sites of each Exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved Exons and 99% of the Exons that lack inactivating mutations match real Exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 Exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.
Eero Vuorio - One of the best experts on this subject based on the ideXlab platform.
-
The Exon Structure of the mouse alpha 2(IX) collagen gene shows unexpected divergence from the chick gene.
The Journal of biological chemistry, 1994Co-Authors: Merja Perälä, Kati Elima, R. Rosati, M Metsäranta, B De Crombrugghe, Eero VuorioAbstract:Abstract One cosmid and two overlapping phage clones covering the entire mouse alpha 2(IX) collagen gene including 12 kilobase pairs (kb) of 5'- and 8 kb of 3'-flanking sequences were isolated from two genomic libraries. The overall gene Structure was determined by restriction mapping and nucleotide sequencing. The gene spans 16 kb from the start of transcription to the polyadenylation site and contains 32 Exons. It codes for a mRNA of 3 kb that translates into a polypeptide of 688 amino acids. The intron-Exon junctions and mRNA Structure were confirmed by amplification of cDNA made for mouse cartilage RNA. The coding sequence of the mouse alpha 2(IX) collagen gene shows marked similarities to those for other type IX collagen chains. Although the overall Exon-intron organization of the mouse gene is very similar to the chick alpha 2(IX) gene, some unexpected differences were observed at the splice junctions. Split codons characteristic for the central triple helical domain of the chick were not found in the mouse gene that thus exhibited a long stretch of Exons with sizes that are multiples of 9 base pairs in this domain. The promoter of the mouse alpha 2(IX) collagen gene contains some G + C-rich elements including three Sp1 consensus recognition sites and a far upstream CCAAT box but no TATAA box. Both primer extension and RNase protection assays revealed several transcription start sites within 418 base pairs of the promoter. The present study reports the first complete nucleotide sequence of any type IX collagen gene and forms the basis for comparative structural studies on this collagen type and for experiments involving transgenic mice.
-
The mouse collagen X gene: complete nucleotide sequence, Exon Structure and expression pattern.
Biochemical Journal, 1993Co-Authors: Kati Elima, Iiro Eerola, R. Rosati, M Metsäranta, Silvio Garofalo, Merja Perälä, B De Crombrugghe, Eero VuorioAbstract:Overlapping genomic clones covering the 7.2 kb mouse alpha 1(X) collagen gene, 0.86 kb of promoter and 1.25 kb of 3'-flanking sequences were isolated from two genomic libraries and characterized by nucleotide sequencing. Typical features of the gene include a unique three-Exon Structure, similar to that in the chick gene, with the entire triple-helical domain of 463 amino acids coded by a single large Exon. The highest degree of amino acid and nucleotide sequence conservation was seen in the coding region for the collagenous and C-terminal non-collagenous domains between the mouse and known chick, bovine and human collagen type X sequences. More divergence between the sequences occurred in the N-terminal non-collagenous domain. Similarity between the mammalian collagen X sequences extended into the 3'-untranslated sequence, particularly near the polyadenylation site. The promoter of the mouse collagen X gene was found to contain two TATAA boxes 159 bp apart; primer extension analyses of the transcription start site revealed that both were functional. The promoter has an unusual Structure with a very low G + C content of 28% between positions -220 and -1 of the upstream transcription start site. Northern and in situ hybridization analyses confirmed that the expression of the alpha 1(X) collagen gene is restricted to hypertrophic chondrocytes in tissues undergoing endochondral calcification. The detailed sequence information of the gene is useful for studies on the promoter activity of the gene and for generation of transgenic mice.
-
Mouse type II collagen gene. Complete nucleotide sequence, Exon Structure, and alternative splicing.
The Journal of biological chemistry, 1991Co-Authors: M Metsäranta, B De Crombrugghe, D Toman, Eero VuorioAbstract:Several overlapping clones covering the entire mouse type II collagen gene including 10 kilobases (kb) of 5'- and 15 kb of 3'-flanking sequences were isolated from a cosmid library. The overall gene Structure was determined by restriction mapping and sequencing. The gene spans 28.9 kb from the start of transcription to the polyadenylation site and contains 54 Exons. It codes for a major mRNA species of 4910 bases which translates into a polypeptide of 1419 amino acids. A less abundant RNA species of 5110 bases contains additional sequences corresponding to an alternatively spliced Exon 2. Except for the amino-terminal propeptide (N-propeptide) domain the Exon-intron organization of the mouse pro alpha 1(II) collagen gene is remarkably similar to genes for other fibrillar collagen types. The overall identity of the coding sequences of the mouse and human type II collagen genes is 89% at the nucleotide level, but only 37 amino acid changes occur within the mature alpha 1(II) collagen chains between mouse and man. Intron sizes are also conserved between the mouse and human genes but not with the chick alpha 1(II) gene. The promoter of the mouse type II collagen gene is similar to those of the rat and human genes containing a TATA box and several G + C-rich elements but no CCAAT box. The 3'-untranslated sequence contains two regions of high homology between chick, mouse, bovine, and human genes preceding the major polyadenylation site. Additional size variation in the mRNA arises from the use of a minor polyadenylation signal. Information on conserved noncoding sequences will help in studies on the regulation of the pro alpha 1(II) collagen gene. Detailed knowledge of the gene is also necessary for site-directed mutagenesis and work with transgenic mice.