Chlamy ESTGenomeBrowser

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Chlamy EST-Genome-Browser
http//www.bioinfolab.org/software/egb/chlamy

• Dr. Chun Liang
• Department of Botany
• Miami University, Ohio, USA

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Acknowledgement

• Collaborators
• Prof. Ji Guoli Automation Department, Ximen
  University, China
• Dr. Thomas Wu Genentech, Inc., South San
  Francisco, USA
• Dr. Mario Stanke University of
  Göttingen, Germany
• Dr. Olivier Vallon Institut de Biologie
  Physico-Chimique, France
• Dr. Jeff Shrager Carnegie Institute of
  Washington
• Dr. Erik F. Y. Hom Department of MCB, Harvard
  University,

Lab Members Ms. Lin Liu Bioinformatician Mr.
Zhixin Zhao Ph.D. Student Mr. Praveen Kumar M.S.
Student Mr. Hanqing Hu Undergraduate Ms. Sara
Savage Undergraduate Mr. Daniel Barret
Undergraduate
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All data are sortable (descending or ascending)
and searchableI. D. M Insertion, Deletion and
MismatchTot. ESTs Total number ESTS in a given
genome positionMutation Num Total ESTs that
have bases different from genomeMutation Ratio
Mutation Num/Tot. ESTs
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3UTR
CDS
SNPs
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Drag and move vertically
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Zoom out
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Drag and move vertically
Intron Retention
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Tab EST
Clone, Lib Search
5 EST
3 EST
Clone Search for 1112 cDNA library 137H07 clone
(intron retention)?
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Tab EST
Clone, Lib Search
5 EST
3 EST
Clone Search for CACW cDNA library 23473 clone
(no intron retention)?
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Sort alignments Asc or Desc
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A
B
C
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50 kbp
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Mutation Len length of the continuous
mutationCategory I (insertion), D (Deletion),
M (Mismatch), X (mix of I, D or M)I. D. M
Mutation Pattern MD means one mismatch followed
by one deletionMutation Ratio Mutation
Num/Tot. ESTs
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• About 20 genes

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On-going Work
1. AUGUSTUS and PASA transcript isoforms 2.
Gene Predictions from other methods or different
versions of the same methods 3. Capability for
454 data and Solexa data integration Transcript
base frequency graph for each genome position

We have provided API (Application Programming
Interfaces) for 1. Sequence Viewer 2.
EST-Genome-Browser
http//www.bioinfolab.org/software/egb/chlamy