Software To Graphically Represent The Splicing In A Simple Way

Question

[Anima Mundi]

Hello everybody. Making a poster, I had the need to represent graphically a series of genes with their splicing in a simple way. I have a series of cDNA variants aligned against their correspondent genomic strand, and I was thinking about summarising the information displaying each genomic region as a thin line, the exons as thicker parts on the genomic region and the introns as graphical hairpins connecting exons (nothing new, very classical way). Is there a software that, given an alignment between a genomic region with its cDNAs (or at least some of them), outputs something like this? I started to do it manually, but the process is both slow and inaccurate.

[Giovanni M Dall'Olio]

this has already been asked previously. See How to visualize splice junction data, in particular exon-skipping, Data visualisation -- exon/intron map?

Answer 1

[Pierre Lindenbaum]

See also

Batch Viewing of UCSC Browser Graphic

here is a XML returned by the UCSC for the table knownGene:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -X -e 'select * from knownGene limit 2'


<resultset statement="select * from knownGene limit 2
" xmlns:xsi="&lt;a href=" http:="" www.w3.org="" 2001="" XMLSchema-instance"="" rel="nofollow">http://www.w3.org/2001/XMLSchema-instance">
  <row>
    <field name="name">uc001aaa.3</field>
    <field name="chrom">chr1</field>
    <field name="strand">+</field>
    <field name="txStart">11873</field>
    <field name="txEnd">14409</field>
    <field name="cdsStart">11873</field>
    <field name="cdsEnd">11873</field>
    <field name="exonCount">3</field>
    <field name="exonStarts">11873,12612,13220,</field>
    <field name="exonEnds">12227,12721,14409,</field>
    <field name="proteinID"></field>
    <field name="alignID">uc001aaa.3</field>
  </row>

  <row>
    <field name="name">uc010nxr.1</field>
    <field name="chrom">chr1</field>
    <field name="strand">+</field>
    <field name="txStart">11873</field>
    <field name="txEnd">14409</field>
    <field name="cdsStart">11873</field>
    <field name="cdsEnd">11873</field>
    <field name="exonCount">3</field>
    <field name="exonStarts">11873,12645,13220,</field>
    <field name="exonEnds">12227,12697,14409,</field>
    <field name="proteinID"></field>
    <field name="alignID">uc010nxr.1</field>
  </row>
</resultset>

if you write your data in that format, you can process the XML file with my XSLT stylesheet to produce a SVG file

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -X -e 'select * from knownGene limit 2' | xsltproc <(curl -s "https://raw.github.com/lindenb/xslt-sandbox/master/stylesheets/bio/ucsc/ucsc-sql2svg.xsl") - | head

<svg:svg xmlns:svg="&lt;a href=" http:="" www.w3.org="" 2000="" svg"="" rel="nofollow">http://www.w3.org/2000/svg" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" width="900" height="41" style="stroke-width:1px;">
  <svg:title>select * from knownGene limit 2 </svg:title>
  <svg:defs>
    <svg:linearGradient x1="0%" y1="0%" x2="0%" y2="100%" id="grad">
      <svg:stop offset="5%" stop-color="black"/>
      <svg:stop offset="50%" stop-color="whitesmoke"/>
      <svg:stop offset="95%" stop-color="black"/>
    </svg:linearGradient>
    <svg:linearGradient x1="0%" y1="0%" x2="0%" y2="100%" id="vertical_body_gradient">

and a result visualized in firefox:

Answer 2

[Charles Warden]

I have heard that the sushimi plot is a new, useful way to visualize splicing events:

http://genes.mit.edu/burgelab/miso/docs/sashimi.html

I haven't had a chance to try out the software yet - let me know what you think!

[Anima Mundi]

It is fine; it took a while for the installation, but once done it provides nice maps.