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Group 2

    Our group powerpoint can be found as an attachment to this page. 

    Division of work:

    Shaylyn did the FGENESH result annotation.

    Shuai did the GeneMark annotation.

    Karthik did AUGUSTUS annotation, and putting everything together. 

    Group Members:

    • Shaylyn Wiarda
      • I am starting my second year of grad school under Dr. Ohm in Plant Breeding and Genetics.  My project is working with the tin gene in a winter wheat background. Email: swiarda@purdue.edu
    • Karthik Padmanabhan
      • I am in Dr. Gribskov's lab doing my second year Ph.D in Computational Biology. I am currently working on plant protein kinase gene modeling. Email: kpadmana@purdue.edu
    • Shuai Chen
      • I am a second year Ph.D student co-advised by Dr. Marisol Sepulveda and Dr. Krista Nichols. My project is to develop Daphnia pulex miRNAs as biomarkers for environmental toxicant and temperature changes.

        Email: chen905@purdue.edu

     

    General workflow:

    1. MegaBLAST

    2. Gene prediction on raw sequence

    1. AUGUSTUS
    2. FGENESH
    3. GeneMark

    3. CpG island prediction using EMBOSS tools

    4. Masking sequence repeats using Repeat Masker

    5. Gene prediction on repeat-masked sequence

    1. AUGUSTUS
    2. FGENESH
    3. GeneMark

    6. BlastX against protein database

    7. BlastN against EST database

    8. Pfam to predict protein domains and function

    9. Blast2GO to identify GO terms of predicted protein models

     

    Preliminary Results:

    • MegaBLAST search strategy excluding Zea mays

     MBexclzmays.jpg

    Notes: Hits mainly from Oryza sativa, top three hits from Zea diploperennis, Zea luxurians, and Gossypium raimondii respectively. 

    Attached file: Search Strategy used (.ASN file)

    • MegaBLAST search strategy vs Zea mays aloneMBvszmays.jpg

    Notes: Hits mainly from chromosomes 5, 6 and 8. 

    Attached file: Search strategy (.ASN file)

    • GeneMark (HMM) results

    Attached file: GeneMark results (.txt file)

    • FGENESH results

    Attached files: Results in plain text (.txt) and a graphical representation (.pdf)

    • AUGUSTUS results

    Augustus_graphical.png

    Attached files: Augustus text ouput, predicted amino acid sequences, and predicted genes.

     

    kpadmana 01 October 2012

     

    • Predicted Gene Summary from GeneMark, FGENESH, AUGUSTUS
      • Gene Number Comparison
          GeneMark FGENESH AUGUSTUS
        Number of Genes 29 23 23*

        *AUGUSTUS has multiple transcripts for gene number 5, 6, 10, 11, 12, 18, and 23.

      • Gene Similarity

     

    GeneMark FGENESH AUGUSTUS
        Sequence       Sequence       Sequence  
    Gene# Exon# Start End Chain Gene# Exon# Start End Chain Gene# Exon# Start End Chain
    1 1 1235 1609 + 1 1 1235 1609 + 1 1 1235 1609 +
    3 5 5202 11176 - 2 3 5202 9653 - 2 2 5202 9776 -
              3 6 10175 19949 - 3 1 10175 11176 - 
    6 5 30054 31691 + 5 7 26051 31691 +          
    8 2 34506 35656 - 6 10 32122 35656 +          
    10 4 43275 46303 + 9 4 43275 46303 + 8 2 43275 46303 +
    12 4 46796 48333 + 10 2 46796 48106 +          
    13 9 48554 51869 - 11 8 48554 51805 - 10.1 8 48554 51636 -
                        10.2 8 48554 51636 -
    14 1 53897 54271 - 12 1 53897 54271 -          
              14 22 64642 70725 - 11.1 21 64642 80738 -
    18 6 75180 80738 - 15 5 74810 80738 - 11.2 22 64642 80738 - 
    20 6 88915 99032 - 16 9 88367 99032 -          
    24 2 125987 126775 - 19 8 118336 126775 - 16 2 125987 126775 -
    26 2 137895 138639 -           22 1 138049 138639 -

    *Similar genes are highlighted with similar colors.

    **Red is the base pair of matching start/end sequences.

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