Instructions for aligning the Chamaecrista transcriptome with the soybean genome

  • The Chamaecrista 1.1 transcriptome has been aligned to the soybean genomes and can be viewed using the SoyBase and the Soybean Breeder's Toolbox. Or use this alternate link to the same site. Steven Cannon at Iowa State University aligned the Chamaecrista transcriptome with soybean in SoyBase.
  • Once you are at Soybase, turn on the Chamaecrista tracks at the bottom of the page

    • You may also want to try aligning the Chamaecrista transcriptome to the soybean genome yourself. Uwe Hilgert at Cold Spring Harbor Lab offers this approach. Go to Phytozome, the soybean genome browser.

    Click 'Browse Genome'.

    Set the tracks in Phytozome by using 'Configure tracks' and turning everything 'Off' except 'transcript.'

    At the bottom of the page, following 'Enter Remote Annotation URL' enter http://pipeline.dnalc.org/files/uwe/sue_Singer02_match_part.gff Select 'Upload URLs'.

  • Under Landmark or Region enter a chromosomal region of interest and see what EST files map to the G. max genome. Try Gm01:500001..590000, Gm01:627000..652000, Gm12:709501..799500, and Gm17:7109501..7199500. Please be aware that the maximum fragment you can view at a time is 90kb.
  • When familiar with the navigation, please click again 'Configure tracks' and check 'BLATX Plant Peptides.' There is a lot of protein evidence to display in this track and it may be worthwhile to only use it for smaller segments, say a couple of genes at the time.
  • Save the spreadsheet at http://pipeline.dnalc.org/files/uwe/sue_singer_blast.xls to your computer and get from it further information about the results of the alignment of your ESTs.
  • Not all sequences in the Chamaecrista transcriptome sequence file (http://pipeline.dnalc.org/files/uwe/sue_singer_file.fasta) can be successfully aligned to the soybean genome. The spreadsheet at http://pipeline.dnalc.org/files/uwe/sue_singer_blast.xls (Worksheet 'by Cf#') may be useful in determining how many of the original 21781 sequence reads actually aligned and whether there is a specific pattern to this (like, whether longer ESTs aligned better than shorter).
    • Record a minimum of two findings from your work aligning the Chamaecrista transcriptome with the soybean genome