TraV: A Genome Context Sensitive Transcriptome Browser
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{"title"=>"TraV: A genome context sensitive transcriptome browser", "type"=>"journal", "authors"=>[{"first_name"=>"Sascha", "last_name"=>"Dietrich", "scopus_author_id"=>"35777738000"}, {"first_name"=>"Sandra", "last_name"=>"Wiegand", "scopus_author_id"=>"55867557400"}, {"first_name"=>"Heiko", "last_name"=>"Liesegang", "scopus_author_id"=>"6602828350"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24709941", "doi"=>"10.1371/journal.pone.0093677", "sgr"=>"84899421862", "scopus"=>"2-s2.0-84899421862", "issn"=>"19326203", "pui"=>"372955982"}, "id"=>"c9cb4291-7ca5-339f-bd0d-0aaf67e02e20", "abstract"=>"Next-generation sequencing (NGS) technologies like Illumina and ABI Solid enable the investigation of transcriptional activities of genomes. While read mapping tools have been continually improved to enable the processing of the increasing number of reads generated by NGS technologies, analysis and visualization tools are struggling with the amount of data they are presented with. Current tools are capable of handling at most two to three datasets simultaneously before they are limited by available memory or due to processing overhead. In order to process fifteen transcriptome sequencing experiments of Bacillus licheniformis DSM13 obtained in a previous study, we developed TraV, a RNA-Seq analysis and visualization tool. The analytical methods are designed for prokaryotic RNA-seq experiments. TraV calculates single nucleotide activities from the mapping information to visualize and analyze multiple transcriptome sequencing experiments. The use of nucleotide activities instead of single read mapping information is highly memory efficient without incurring a processing overhead. TraV is available at http://appmibio.uni-goettingen.de/index.php?sec=serv.", "link"=>"http://www.mendeley.com/research/trav-genome-context-sensitive-transcriptome-browser", "reader_count"=>71, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>18, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>13, "Student > Bachelor"=>3, "Lecturer"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>18, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>13, "Student > Bachelor"=>3, "Lecturer"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>43, "Medicine and Dentistry"=>2, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>6, "Immunology and Microbiology"=>3, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>1, "United Kingdom"=>1, "Slovenia"=>1, "Germany"=>3}, "group_count"=>4}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1452728"], "description"=>"<p>Identified UTRs and Free Transcripts in <i>B. licheniformis</i> DSM13.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks", "utrs", "transcripts"], "article_id"=>989292, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.t001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identified_UTRs_and_Free_Transcripts_in_B_licheniformis_DSM13_/989292", "title"=>"Identified UTRs and Free Transcripts in <i>B. licheniformis</i> DSM13.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-07 03:14:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1452725"], "description"=>"<p>In case that the available mapped read data does not contain strand specificity information TraV can be switched into the strand unspecific mode in which all mapped reads are summed up to an general activity of a genome locus.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks", "unspecific"], "article_id"=>989289, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strand_unspecific_mode_of_TraV_/989289", "title"=>"Strand unspecific mode of TraV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-07 03:14:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1452722"], "description"=>"<p>Differential expression of genes BLi00261 and BLi00262 at selected time points of a fermentative process. Dataset L-I shows the transcriptional activity of <i>B. licheniformis</i> DSM13 at the early exponential growth phase, L-III shows the transcriptional activity at the end of the exponential growth phase and L-V shows the transcriptional activity at the late stationary phase.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks"], "article_id"=>989286, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_/989286", "title"=>"Differential expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-07 03:14:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1452727"], "description"=>"<p>(<b>A</b>) 5′UTR of annotated gene feature. (<b>B</b>) Antisense transcript. (<b>C</b>) Transcriptional activity at a non-annotated region (free transcripts). A, B and C also show strong increases in transcriptional activity, which TraV predicts as transcription start sites. All graphs shown represent data from RNA-Seq experiments performed on <i>B. licheniformis</i> DSM13 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093677#pone.0093677-Wiegand1\" target=\"_blank\">[9]</a> (indicated by red boxes). All graphs shown represent data from RNA-Seq experiments performed on <i>B. licheniformis</i> DSM13 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093677#pone.0093677-Wiegand1\" target=\"_blank\">[9]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks", "visualized"], "article_id"=>989291, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.g005", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Patterns_visualized_by_TraV_/989291", "title"=>"Patterns visualized by TraV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-07 03:14:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1452726"], "description"=>"<p>Transcriptional activities are displayed at single nucleotide resolution. The interactive graphic allows access to coverage information as well as to distinct base distances between the selected base (grey marker) and any other base of the displayed sequence. In the example perfect −10 and −35 boxes of a sigma70 promoter are visible.</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks"], "article_id"=>989290, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Magnification_view_of_TraV_/989290", "title"=>"Magnification view of TraV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-07 03:14:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1452720"], "description"=>"<p>Transcriptional activity is depicted by graphs (red graph representing positive strand, blue representing negative strand). Annotated genome information is represented by black arrows. User-provided GFF-based annotations are represented in tracks between the original genome information by coloured arrows (green arrow in this figure).</p>", "links"=>[], "tags"=>["Biochemistry", "Nucleic acids", "nucleotides", "Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "genomics", "Functional genomics", "microbiology", "Computer applications", "Web-based applications", "Network Analysis", "Regulatory networks"], "article_id"=>989284, "categories"=>["Biological Sciences"], "users"=>["Sascha Dietrich", "Sandra Wiegand", "Heiko Liesegang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0093677.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_display_of_TraV_/989284", "title"=>"Main display of TraV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-07 03:14:14"}

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Relative Metric

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