Tool for loci localization on chromosomes

Dolphin22

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Join Date: Jul 2012

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#1

Tool for loci localization on chromosomes

09-19-2013, 04:29 AM

Hey everybody.

I am looking for a tool to visualize specific loci on chromosomes structures of Arabidopsis thaliana. The result shoulb something like this.

Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa) - BMC Genomics

http://www.biomedcentral.com/1471-2164/13/253/figure/F4?highres=y

Background CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family represented by 68 members in Arabidopsis and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has not been studied in the model tree species Populus to date. Results In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in Populus was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in Populus, of which most contained more than one CCCH motif and a type of non-conventional C-X11-C-X6-C-X3-H motif was unique for Populus. All of the Populus CCCH genes were phylogeneticly clustered into 13 distinct subfamilies. In each subfamily, the gene structure and motif composition were relatively conserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of 90, 90 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairs were identified in Populus, of which 22 pairs (64.7 %) might be created by the whole genome segment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91 CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3 typical RNA-binding proteins. The expression profiles of all Populus CCCH genes have been digitally analyzed in six tissues across different developmental stages, and under various drought stress conditions. A variety of expression patterns of CCCH genes were observed during Populus development, of which 34 genes highly express in root and 22 genes show the highest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR (RT-qPCR) was further performed to confirm the tissue-specific expression and responses to drought stress treatment of 12 selected Populus CCCH genes. Conclusions This study provides the first systematic analysis of the Populus CCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion of Populus CCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members of Populus CCCH gene family. Particularly, some CCCH genes may be involved in wood development while others in drought tolerance regulation. Our results presented here may provide a starting point for the functional dissection of this family of potential RNA-binding proteins.

Is there a tool that you can recommend?

Thank you for your replies in advance
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LeightonP

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Join Date: Feb 2011

Posts: 29
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#2

09-19-2013, 06:58 AM

Biopython has a Chromosome module for drawing the basic shapes with annotation:

Biopython Tutorial and Cookbook

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc277

but for the lines connecting markers, you might need Ilustrator or similar.
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