GMOD/Apollo: Apollo2.1.0(JB#d3827c)

<p><strong>2.1.0 Official Release</strong></p> <p>Some of the new features include:<br> - Added ability to annotate a variant from VCF evidence tracks [1892](https://github.com/GMOD/Apollo/pull/1892)<br> - Allow forced assignment of transcript to a gene [#1851](https://github.com/GMOD/Apollo/pull/1851)<br> - Added proper Instructor and Organism Admin permission level [#1178](https://github.com/GMOD/Apollo/issues/1178)<br> - Indicate start / stop codons with color [#1852](https://github.com/GMOD/Apollo/pull/1852)<br> - Set the default biotype on track [#1861](https://github.com/GMOD/Apollo/issues/1861)</p> <p>Some important bug fixes:<br> - Prevents setting bad translation starts and ends [#1838](https://github.com/GMOD/Apollo/issues/1838)<br> - Fixed descriptor leak when loading bulk loading GFF3 [#1187](https://github.com/GMOD/Apollo/pull/1887)<br> - Fixed adding ability to create sequence alterations of uneven length [#1883](https://github.com/GMOD/Apollo/issues/1883)<br> - Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case [#1879](https://github.com/GMOD/Apollo/issues/1879)<br> - In some cases when the name store is not properly configured, the location is not remembered [#1895](https://github.com/GMOD/Apollo/issues/1895)</p> <p><br> *Note* You will need to [install node 6 or better](https://nodejs.org/en/download/package-manager/).  <br> *Note* If updating your jbrowse settings from previous versions in `apollo-config.groovy` you will need to set the JBrowse to use the [currently tagged version or better](https://github.com/GMOD/Apollo/blob/master/sample-postgres-apollo-config.groovy#L113).   If this is  commented out, however, [the default will work](https://github.com/GMOD/Apollo/blob/master/grails-app/conf/Config.groovy#L388-L433). <br> *Note* Some issues with new tomcat and addStore / addTracks RFC 7230 and RFC 3986.  See http://genomearchitect.readthedocs.io/en/latest/Setup.html?highlight=RFC#json-in-the-url-with-newer-versions-of-tomcat</p> <p>The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md</p> <p>Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/stable/</p> <p>Note: You can find a guide upgrading existing Apollo installations here: <br> http://genomearchitect.readthedocs.io/en/stable/Migration.html</p> <p>Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/</p> <p>Active mailing list ([email protected]) and [archive](http://gmod.827538.n3.nabble.com/Apollo-f815553.html).</p

D. melanogaster Intron Lengths Are Highly Correlated with Their Inferred D. pseudoobscura Orthologs; D. melanogaster Paralogous Introns Show No Such Correlation

<p>(A) <i>x</i>-axis, length (log₁₀) of annotated D. melanogaster introns; <i>y</i>-axis, length (log₁₀) of their inferred orthologs in the D. pseudoobscura genome. Red circles indicate those introns containing a transposon in <i>D. melanogaster;</i> blue circles indicate those introns containing a transposon in <i>D. pseudoobscura;</i> gold circles indicate introns without identifiable transposons in either species. Spearman correlation coefficient: 0.637; <i>p</i> < 0.001.</p> <p>(B) Intron lengths of paralogs having the same intron–exon structure as judged by the positions of their splice junctions relative to the protein alignments of their reciprocal best-hit best HSPs. <i>x</i>-axis, length (log₁₀) of introns in an annotated D. melanogaster gene; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns. Spearman correlation coefficient: 0.448; <i>p</i> < 0.001.</p

Intron Lengths Can Be Used as a Molecular Clock

<p><i>y</i>-axis, magnitude of the Spearman correlation coefficient for the five <i>Drosophila</i> distributions shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-g008" target="_blank">Figure 8</a>. <i>x</i>-axis, time (millions of years) since last common ancestor based on protein similarities as calculated in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Black bars above and below each data point denote observed variance in the data and were obtained by randomly resampling 1,000 orthologous intron pairs 100 times. Best-fitting curve (shown in black) y = −0.0057x + 0.9266; R² = 0.9875.</p

Cumulative Distribution Functions Illustrating Proteome-Wide Trends in Protein Similarity

<p><i>x</i>-axis, bits/aligned position; <i>y</i>-axis, cumulative fraction of HSPs having that number of bits/aligned amino acid pair or less. To facilitate display, only a subset of the 21 possible pair-wise combinations is shown. Data are based upon all reciprocal best BLASTP hits identified in all versus all BLASTP searches of the proteomes. Similarity calculations were restricted to the high-scoring HSP for each BLAST hit, in order to avoid data duplication due to overlapping alignments.</p> <p>There were 13,339 <i>M. musculus–H. sapiens</i> reciprocal best hits; 6,435 between D. melanogaster and <i>A. gambiae;</i> 5,828 between C. intestinalis and <i>H. sapiens;</i> 5,542 between D. melanogaster and <i>H. sapiens;</i> 4,669 between C. elegans and <i>H. sapiens;</i> 4,588 between C. elegans and <i>D. melanogaster;</i> 3,361 between H. sapiens and <i>A. thaliana;</i> and 2,835 between C. elegans and A. thaliana.</p> <p>atha, <i>A. thaliana;</i> cele, <i>C. elegans;</i> cint, <i>C. intestinalis;</i> dmel, <i>D. melanogaster;</i> hsap, <i>H. sapiens;</i> mmus, <i>M. musculus.</i></p

Neighbor-Joining Trees Summarizing Proteome-Wide Trends in Protein Similarity and Genome-Wide Trends in Intron–Exon Structural Similarity

<p>Proteome-wide trends in protein similarity (A), and genome-wide trends in intron–exon structural similarity (B). Numbers beneath tree nodes are bootstrap values.</p

Controlling for the Impact of Unequal Rates of Protein Evolution on the Evolution of Intron–Exon Structures

<p>(A) Unrooted neighbor-joining tree based upon amino acid similarities for reciprocal best-hit best HSPs having 1.25 bits/aligned amino acid pair.</p> <p>(B) Unrooted neighbor-joining tree based upon similarities in the intron–exon structures of those same HSPs.</p

Lengths of Orthologous Introns within a Quartet Are More Correlated than Those of Paralogous Introns

<p>(A) Quartet orthologous intron pairs. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding orthologous introns in the mouse member of the same quartet. Spearman correlation coefficient: 0.903; <i>p</i> < 0.001.</p> <p>(B) Paralogous introns. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns in the other human member of the same quartet. Spearman correlation coefficient: 0.140; <i>p</i> < 0.001. The mouse distributions are essentially identical to their human counterparts.</p

Global Overview of Gene Structure in Six Annotated Animal Genomes

<p>(A) Intron length. Annotated intron length (log₁₀) is plotted on the <i>x</i>-axis; the frequency at which introns of that length occur in an organism's genome is plotted on the <i>y</i>-axis.</p> <p>(B) Exon length. <i>x</i>-axis, coding-exon length in nucleotides; <i>y</i>-axis, frequency.</p> <p>(C) Intron density. A transcript's intron density is equal to its number of coding introns divided by the length of the protein it encodes. <i>y</i>-axis, frequency of annotated transcripts with a particular intron density. <i>x</i>-axis, intron density binned in increments of 0.5 introns/100 amino acid (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a>). Deuterostomes are shown in shades of blue; protostomes in shades of red.</p

Correlation in Orthologous Intron Lengths Is Proportional to Time since Last Common Ancestor

<p>From left to right, and top to bottom: Annotated D. melanogaster lengths (<i>x</i>-axis) versus inferred orthologous intron lengths (<i>y</i>-axis) for D. simulans (strain 6), <i>D. yakuba, D. ananassae, D. pseudoobscura,</i> and D. virilis.</p> <p>Bottom right-hand panel: Annotated D. melanogaster lengths (<i>x</i>-axis) versus inferred A. gambiae intron lengths (<i>y</i>-axis). Approximate time since last common ancestor is shown in red in the lower left-hand corner in each panel; these are approximate estimates based upon protein data [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Spearman correlation coefficients: 0.886, 0.863, 0.670, 0.637, 0.550, and 0.410 for <i>D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis,</i> and A. gambiae distributions, respectively. <i>p</i> < 0.001 for each correlation coefficient. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a> for analysis details.</p

Intron–Exon Structures Evolve Largely Independently of Protein Sequences

<p><i>x</i>-axis, human reciprocal best-hit best HSPs for four representative proteomes binned by percent identity in 5% increments. <i>y</i>-axis, percent of aligned introns among the HSPs in each bin.</p> <p>cele, <i>C. elegans;</i> cint, <i>C. intestinalis;</i> dmel, <i>D. melanogaster;</i> hsap, <i>H. sapiens;</i> mmus, M. musculus.</p