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Group 1

    Analysis can be found on "Work in Progress" and specific Gene pages

    Members

    Tyler Tiede

    2nd year Ph.D student in the Agronomy Department's Plant Breeding and Genetics program, working in the Rocheford lab on maize grain nutritional traits. Email: tiede@purdue.edu

    Jenae Skelton

    3rd year Ph.D. student in Dr Ohm's wheat breeding lab looking at wheat root architecture traits. Email: skelton@purdue.edu.

    Yanzhu Ji

    3rd-year PhD student from Dr. Andrew DeWoody's lab in Forestry and Natural Resources. We focuses on molecular evolution of non-model organisms.  Email: ji20@purdue.edu

    Intrinsic Sequence Analysis

     

    Presentation Download

    PDF of project presentation here

    Summary

    From the analysis conducted so far the pieces of the overall story are starting to come together. The instrinsic sequence characteristics revealed some problematic areas in the sequence. The dot plot revealed some areas, summarized on the "work in progress" page and those areas correspond well to regions that were masked by RepeatMasker; masked regions largely consisted of long terminal repeat (LTR) retrotransposons Copia and DIRS1 (see review). Further investigation of the intrinsic nature of the sequence revealed that, before masking, the sequnce had a GC content of 50%, which is higher than the 46.5%genome-wide average. This suggest that our region may be slighltly enriched for genes.

    Plotting the CpG islands provides some insight into possible gene locations, and in fact the gene predictors FGeneSH, GeneMark, and AUGUSTUS all predict genes that agree with some of the CpG islands. A brief look at the summaries of the gene predictor results shows that the same genic regions were predicted, for the most part. This provides promising evidence that there is, in fact, a gene in that region worth investigating and that further analysis is needed to determine the real characteristics of the genes, such as where the transcription start site actually is, where the exons and introns are, splice site locations and alternatively splice variants, etc... Plans moving forward include looking at EST, cDNA, and protein data to glean this information. More intrinsic analysis may also help us understand these particular characteristics in more detail.

     

    The gene annotations can be viewed on sub-pages titled "Gene 1" ... "Gene 5"

     

    Group Work: Tyler processed the majority of the analyses and gave our presentation. He also finished the powerpoint presentation. Yanzhu ran the repetitive regions anaylsis and made the slides for that section. I ran a blast search on our sequence, but I narrowed the parameters too much and got a wrong conclusion. We kept that blast search as a subpage of the "Supplemental Analysis" page, but we used Tyler's analyses instead. I started the powerpoint and made the introductory slides and started slides for each gene, which Tyler added to and corrected as necessary. All three of us met several times to go over each others' analyses and annotations to decide how to interpret the output and what conclusions we could make confidently. Tyler was very helpful in explaining how to run the programs correctly when Yanzhu or I were not familiar with them.

    skelton 6 Dec 2012

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     Group 1 Gene Annotation Project presentation.pdf
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    1553.7 kB09:42, 6 Dec 2012tiedeActions
     seq1.fa.txt
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    152.36 kB16:49, 17 Sep 2012gribskovActions
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