Evidence for Active Maintenance of Inverted Repeat Structures Identified by a Comparative Genomic Approach
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{"title"=>"Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach", "type"=>"journal", "authors"=>[{"first_name"=>"Guoyan", "last_name"=>"Zhao", "scopus_author_id"=>"55478879700"}, {"first_name"=>"Kuan Y.", "last_name"=>"Chang", "scopus_author_id"=>"35761045100"}, {"first_name"=>"Katherine", "last_name"=>"Varley", "scopus_author_id"=>"25637900800"}, {"first_name"=>"Gary D.", "last_name"=>"Stormo", "scopus_author_id"=>"7005191518"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-55349100534", "pui"=>"352606040", "doi"=>"10.1371/journal.pone.0000262", "sgr"=>"55349100534", "pmid"=>"17327921", "issn"=>"19326203"}, "id"=>"59a22c2a-f3d3-388e-a674-f2ca5158cd07", "abstract"=>"Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of C. elegans genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of C. briggsae and C. remanei show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.", "link"=>"http://www.mendeley.com/research/evidence-active-maintenance-inverted-repeat-structures-identified-comparative-genomic-approach", "reader_count"=>29, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>2, "Taiwan"=>1, "United Kingdom"=>2, "Germany"=>1, "Russia"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/952336"], "description"=>"<p>An example of divergently oriented inverted repeat. A. Schematic representation of the inverted repeat structure of the <i>C. elegans</i> F44E5.4 - F44E5.5 genomic region, CBG13233 - CBG13234 genomic region in <i>C. briggsae</i> and Contig35.Fgenesh-Celegans.59.final (Contig35-1) - Contig35.eannot.383.final.final (Contig35-2) region in <i>C. remanei</i>. B. Sequence comparison was carried out between sequence 1 and sequence 2 for each row. Sequence identity within each species (intraspecies) in a global alignment (Needleman-Wunsch) is shown in the last column of the table. C. Sequence identity between species (interspecies) is shown in the last column of the table. Sequence identity within a species is much higher than the sequence identity between species. CE: <i>C. elegans</i>; CB: <i>C. briggsae</i>; CR: <i>C. remanei</i>; IGR: intergenic region. * indicates that sequence identity could be higher than 88.5% because Contig35-2 has a stretch of Ns (10) which is estimated length of the sequencing gap.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "genetics and genomics/comparative genomics"], "article_id"=>622648, "categories"=>["Medicine", "Genetics"], "users"=>["Guoyan Zhao", "Kuan Y. Chang", "Katherine Varley", "Gary D. Stormo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000262.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_1_/622648", "title"=>"Figure 1", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:44:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/952586"], "description"=>"<p>Duplication and evolution of inverted repeat orthologous gene pairs. A. Duplication of inverted repeat gene pair in <i>C. briggsae</i>. The CBG13233 - CBG13234 genomic region, which is orthologous to the <i>C. elegans</i> F44E5.4 - F44E5.5 genomic region, is duplicated as tandem repeats in <i>C. briggsae</i>. Number shows sequence identity between two sequences in a global alignment. Number in parenthesis shows sequence identity between two sequences in a local alignment. CBG13231 and CBG13233 are 99.3% identical for the first 297 nt. CBG13232 and CBG13234 are 99.2% identical for the first 764 nt. CBG13231 and CBG13232 are 100% identical for the first 297 nt. The intergenic region between CBG13231 and CBG13232 are 98% identical to the intergenic region between CBG13233 and CBG13234. B. Duplication of inverted repeat gene pair in <i>C. remanei</i>. The Contig35.Fgenesh-Celegans.59.final (Contig35-1) - Contig.eannot.388.final.final (Contig35-2) region, which is orthologous to the <i>C. elegans</i> F44E5.4 - F44E5.5 genomic region, is duplicated in <i>C. remanei</i>. Currently, it is not clearly whether the duplicated regions are in the same chromosome or not. Sequence identities between duplicated genes as well as between duplicated intergenic sequences are shown in the boxes.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "genetics and genomics/comparative genomics"], "article_id"=>622894, "categories"=>["Medicine", "Genetics"], "users"=>["Guoyan Zhao", "Kuan Y. Chang", "Katherine Varley", "Gary D. Stormo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000262.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_3_/622894", "title"=>"Figure 3", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:46:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/952647"], "description"=>"<p>Duplication and evolution of inverted repeat gene pairs. A. Schematic representation of the genomic structure of the F42F12.1-F42F12.9 gene pairs as well as two <i>C. elegans</i> paralogous gene pairs, four <i>C. briggsae</i> orthologous gene pairs and three <i>C. remanei</i> orthologuos gene pairs. Numbers above each gene pair indicate the sequence identities between the two coding genes in a global alignment. Numbers below each gene pair indicate the sequence identifies between two arms of the inverted repeat intergenic region. Number in parenthesis shows sequence identity between the two sequences in a local alignment. B. Sequence identify between coding sequences. C. Sequence identity between intergenic sequences. For each row, sequence comparison was performed between sequence 1 and sequence 2 and sequence identity between these two sequences is shown in the last column. Contig59-1: Contig59.Fgenesh_Celegans.40.final; Contig59-2: Contig59.eannot.1190.final.final; Contig25-1: Contig25.Fgenesh_Celegans.92.final; Contig25-2: Contig.1332.final.final; Contig25-3: Contig25.Fgenesh_Celegans.94.final; Contig25-4: Contig.1333.final.final. CE: <i>C. elegans</i>; CB: <i>C. briggsae</i>; CR: <i>C. remanei</i>.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "genetics and genomics/comparative genomics"], "article_id"=>622966, "categories"=>["Medicine", "Genetics"], "users"=>["Guoyan Zhao", "Kuan Y. Chang", "Katherine Varley", "Gary D. Stormo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000262.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_4_/622966", "title"=>"Figure 4", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:46:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/952438"], "description"=>"<p>An example of convergently oriented inverted repeat. A. Schematic representation of the inverted repeat structure of <i>C. elegans</i> T27E4.3 - T27E4.9 genomic region as well as <i>C. briggsae</i> and <i>C. remanei</i> orthologous genomic region. In <i>C. elegans</i>, the region of T27E4.8, IGR-1, T27E4.3 and IGR-L is a perfect mirror image of the region of T27E4.2, IGR-2, T27E4.9 and IGR-R. In <i>C. remanei</i>, Contig904-snap.9.final (Contig904-1), Contig904-eannot.018.final.final (Contig904-2), Contig904.eannot.1017.final.final (Contig904-3) and Contig904.snap.4.final (Contig904-4) have similar inverted repeat structure. In <i>C. briggsae</i>, CBG04605, CBG04606, CBG04607 and CBG04608 are arranged in the same orientation but don't have inverted repeat structure. B. Sequence comparison was carried out between sequence 1 and sequence 2 for each row. Sequence identity within each species (intraspecies) in a global alignment (Needleman-Wunsch) is shown in the last column of the table. C. Sequence identity between species (interspecies) is shown in the last column of the table. Sequence identity within a species is much higher than the sequence identity between species for <i>C. elegans</i> and <i>C. remanei</i>. CE: <i>C. elegans</i>; CB: <i>C. briggsae</i>; CR: <i>C. remanei</i>; IGR: intergenic region.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "genetics and genomics/comparative genomics"], "article_id"=>622754, "categories"=>["Medicine", "Genetics"], "users"=>["Guoyan Zhao", "Kuan Y. Chang", "Katherine Varley", "Gary D. Stormo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000262.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_2_/622754", "title"=>"Figure 2", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:45:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/469848"], "description"=>"<div><p>Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of <em>C. elegans</em> genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of <em>C. briggsae</em> and <em>C. remanei</em> show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.</p></div>", "links"=>[], "tags"=>["inverted", "structures", "identified", "comparative", "genomic"], "article_id"=>152599, "categories"=>["Medicine", "Genetics"], "users"=>["Guoyan Zhao", "Kuan Y. Chang", "Katherine Varley", "Gary D. Stormo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000262", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evidence_for_Active_Maintenance_of_Inverted_Repeat_Structures_Identified_by_a_Comparative_Genomic_Approach/152599", "title"=>"Evidence for Active Maintenance of Inverted Repeat Structures Identified by a Comparative Genomic Approach", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-02-28 00:43:19"}

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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2007-01-01T00:00:00Z", "end_date"=>"2007-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[306, 635, 847, 977, 1082, 1179, 1269, 1359, 1441, 1529, 1615, 1685, 1761, 1835, 1900, 1991, 2054, 2126, 2197, 2267, 2338, 2407, 2461, 2518, 2578, 2632, 2691, 2749, 2808, 2862, 2933, 2982, 3027, 3097, 3154, 3206, 3273, 3330, 3380, 3441, 3487, 3539, 3588, 3638, 3689, 3742, 3790, 3838, 3877, 3937, 4002, 4073, 4141, 4191, 4246, 4304, 4367, 4423, 4486, 4536, 4596, 4654, 4727, 4817, 4878, 4943, 5025, 5102, 5170, 5250, 5318, 5386, 5451, 5531, 5582, 5646, 5699, 5773, 5838, 5898, 5957, 6032, 6090, 6165, 6229]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[280, 643, 899, 1064, 1155, 1275, 1371, 1449, 1522, 1610, 1682, 1741, 1803, 1860, 1929, 2033, 2110, 2176, 2251, 2307, 2370, 2424, 2475, 2557, 2619, 2706, 2779, 2841, 2890, 2965, 3028, 3111, 3171, 3216, 3270, 3315, 3364, 3428, 3493, 3551, 3607, 3660, 3703, 3749, 3790, 3834, 3896, 3950, 4000, 4038, 4087, 4151, 4194, 4278, 4316, 4361, 4406, 4476, 4548, 4592, 4661, 4711, 4775, 4848, 4913, 4964, 5046, 5134, 5198, 5301, 5401, 5492, 5571, 5640, 5693, 5750, 5799, 5846, 5897, 5969, 6039, 6065, 6124, 6186, 6249]}]}
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