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-   -   Comparing structure of homologous genes (http://seqanswers.com/forums/showthread.php?t=26958)

manojdarolia 01-29-2013 09:16 AM

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

Gig77 01-29-2013 04:32 PM

Have a look at FeatureStack. Disclaimer: I am author of this program.

GenoMax 01-30-2013 03:19 AM

Quote:

Originally Posted by Gig77 (Post 95013)
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.

GenoMax 01-30-2013 03:23 AM

Quote:

Originally Posted by manojdarolia (Post 94982)
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.

Gig77 01-30-2013 05:31 AM

Quote:

Originally Posted by GenoMax (Post 95059)
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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