After obtaining the sequences of 10 different PCR products for a specific matK region, I need to try to compare, analyze and obtain the different proteins involved. I don't know if I am being clear enough but I really need help.
You can download trial versions of CLC genomic workbench, Geneious or Sequencher from links below to analyze your sequences
http://genecodes.com/demo-download
http://www.geneious.com/web/geneious/download-geneious
http://www.clcbio.com/products/clc-genomics-workbench/
I think expasy webite has more than sufficiient tools to analyse the data
http://www.expasy.org/proteomics
check out the tool description to search your analysis of interest.
All the best.
How large is the region you sequenced? I would start with a simple sequence alignment to see how similar/different the nucleotide/amino acid sequences are. Try just pasting your sequences into the clustal web submission form. Are you interested in the phylogenetic relationships between plant species? If so clustal can also generate a simple tree for you. Not the most rigorous analysis but a good place to start.
-G
Bioedit or chromas are freely available tools to compare and analyse sequencing data
Their are many software for example:
Docking, Molecular Dynamics studies, protein-protein interaction studies, and many web based tools and databases are available like NCBI, EMBL, EBI, DDBJ.
You just switch to expasy proteomic server there you find no of tools to analyze your sequences based on your requirement and properties of your protein seq you can select a tool
As you are working with presumbly interrelated lines of plants, the differences may be rare and small. BioEdit will thus give you a quick answer. If you see any polymorphisms, you can then still try and see whether they have any consequences at all on the amino acid level with other software mentioned (but presumably the changes don't have grave consequences, though).
You could try VectorFriends at http://www.vectorfriends.com
It supports Muscle and Clustalw and is free for academic researchers
I suggest bioedit at the bigning and latter you can compare with the other tools.
Hi,
you can perform sequence similarity to check the similarity between the sequences you got, by doing this you'll get an idea which part of your protein or to be more clear the domain olays an important role in the functioning of the protei. It could done using bioinformatics tools. You can compare sequences using tools like ClustalOmega, T-coffee, Pymol, etc. Hope this helps.
Regards
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