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Old 01-29-2013, 09:16 AM   #1
manojdarolia
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Default Comparing structure of homologous genes

I have few genes for a grass species. now I want to compare the structure of these genes (like length of gene and protein, no. of exons and introns, size of exons and introns, GC content in these regions, etc) with their homologs from other sequenced genomes. Any suggestions or softwares that can do this analysis in one go? Thank you
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Old 01-29-2013, 04:32 PM   #2
Gig77
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Have a look at FeatureStack. Disclaimer: I am author of this program.
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Old 01-30-2013, 03:19 AM   #3
GenoMax
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Quote:
Originally Posted by Gig77 View Post
Have a look at FeatureStack. Disclaimer: I am author of this program.
Is it this paper: http://bioinformatics.oxfordjournals...nt/28/23/3137?

This software is for visualizing the comparisons when one has the gene data on hand, correct? OP wants to find and then display this information.
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Old 01-30-2013, 03:23 AM   #4
GenoMax
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Quote:
Originally Posted by manojdarolia View Post
I have few genes for a grass species. now I want to compare the structure of these genes (like length of gene and protein, no. of exons and introns, size of exons and introns, GC content in these regions, etc) with their homologs from other sequenced genomes. Any suggestions or softwares that can do this analysis in one go? Thank you
Mauve (http://gel.ahabs.wisc.edu/mauve/) is worth a try, if your target genomes are not very dissimilar.

You could also use blast/blat searches, identify the homologous regions in new genomes and then use the software in post #2.
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Old 01-30-2013, 05:31 AM   #5
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Is it this paper: http://bioinformatics.oxfordjournals...nt/28/23/3137?

This software is for visualizing the comparisons when one has the gene data on hand, correct? OP wants to find and then display this information.
Yes, that is correct. You need to have gene models first.
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comparative genomics, genomics, plant genomics

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