Question: Contigs to gene
0
gravatar for aswathy.s
2.9 years ago by
aswathy.s0
aswathy.s0 wrote:

Hi,

I wanted to know How can I get individual complete gene sequences from metagenomics assembled contigs. I have done following steps:

  1. metagenomics assembly of a sample using Ray-Meta.
  2. ORF prediction doen on all contigs
  3. Predicted ORF has used for BLASTX
  4. Protein Functional and Organism annotation based top blastx hits. Now I want to get the gene sequences of top hits. For example, I am interested to get a gene sequence corresponding to amylase of Vibrio neptunius, which is the top hit of BLASTX.

Since I have done BLASTX, using the genebank ID I can get the genepept info, see the link below , but not able to get the gene sequence. http://www.ncbi.nlm.nih.gov/protein/WP_045977982

Please answer me if any have some ideas.

Thanks, Aswathi

blast assembly gene • 881 views
ADD COMMENTlink modified 2.9 years ago by Sej Modha4.2k • written 2.9 years ago by aswathy.s0
0
gravatar for Sej Modha
2.9 years ago by
Sej Modha4.2k
Glasgow, UK
Sej Modha4.2k wrote:

You could use any methods suggested on this thread.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Sej Modha4.2k
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