I have compared two assembled transcriptomes to find out the difference between those two with the use of Progressive Mauve. After completing the genomic comparison and the alignment, it created a output file. Usually i use BIOEDIT to open the file and to do the rest of the analysis. Because of the large data capacity this time it is not possible to open it in the BIOEDIT...
Please anyone help me to figure this out...???????
Thanks... !!!
Hi,
Bioedit is a discontinued software, so it could not adapted to manage high level of data.
You could check if one of this pieces of software (multi-platform, available for windows too) could fit you need :
- aliview: http://www.ormbunkar.se/aliview/
- chromas: http://technelysium.com.au/wp/chromas/ (only for windows)
- snapgene viewer: http://www.snapgene.com/products/snapgene_viewer/
- genomecompiler: http://www.genomecompiler.com
- Ugene: http://ugene.net (more complete than others, amazing tool when you know how to use its features)
I hope this would help you.
Thanks for your kind reply... I'm really new to this area of research...!
Sanpgene didn't work well, just crashed without giving any hint... ! :(
Chromas didn't recognized the file type that i wanted to open... ! :(
Aliview, is also like the Chromas... :(
Genomecompiler didn't install well ... :(
Only hope with Ugene, itz loading...slowly ... probably it will work.. !
JAlign is a good tool for alignment visualization, but in your specific case i would suggest a different approach as you are working with transcriptome, and not genome (which is the focus of Mauve). In my opinion, first you would have to group orthologous genes into clusters, an then perform the alignment. For the clustering i would suggest GET_HOMOLOGUES_EST, and then, for each cluster, do an alignment using MUSCLE.
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