Is There Any Automatic Tool To Compare Paralogous/Orthologous Genes Structure ?

Question

[Mchimich]

Hello everybody ! I have a list of thousand of paralogs genes sequences and I want to compare the structure of the pairs (paralogs) using fasta or GFF file. I'm wondering if there is a automatic tool or script that can do that. For exemple, I would like to know the differences on Exon/Intron structure or the structural variation between the paralogs (Duplication, indels, inversions...). Thanks for your Help.

[Manu Prestat]

What is the specificity of this task comparing to orthology?

[Mchimich]

I would like to see what happens to genes after duplication event regarding their structure.

Answer 1

[justinhaselbach]

Possibly the following links are going to help you for exon- intron structure predictions:

1, http://genes.mit.edu/genomescan.html 2. http://genes.mit.edu/GENSCAN.html 3. http://www.cbs.dtu.dk/services/NetGene2/ 4.http://genome.crg.es/astalavista/ 5. http://t.caspur.it/ASPIC/

For others, for each of the desirable results, one may wish to go fro different suites- for example, why not have some platforms like DNA-Star, CLC Bio, Geneious, Unipro Ugene etc. fort that large-scale edge- that not only analyzes but also allows visualization to find out what's going on with those paralogs.

[Mchimich]

Thanks for your reply ! I have a look on the tools that you provide me but unfortunately I can not run thousand of genes online ! The only tools that use command line is NextGene2 but it concern only human, C. elegans and A. thaliana DNA. DNA-Star, CLC Bio...are commercial software :(

Answer 2

[justinhaselbach]

To visualize or enlist the differences ? And paralogs (of microbial, plant or animal sources?) because.......?

[Eric Normandeau]

Hi Justin. This is clearly not an answer to the original question. You should post a 'comment' instead of an 'answer' in such cases.

[justinhaselbach]

Agree Eric ! Newbie in here. So will rectify ! Thanks a loads.

[Mchimich]

Thanks for answer ! I't's to enlist automatically the differences. Never mind the biological models. Because I want to use a fasta or Gff file of the genes.