How to extract nucleotide sequeces from tblastx table

Yangan · 05-03-2016, 05:56 AM

Hi there,

I am a new learner of bioinformatics.
I used Trinity to do de novo transcriptome assembly then imported the assembly.fasta file into CLC genomeworkbench 7.0.3 to run tblastx using this assembly file as local database while using all P450 cDNA of Arabidopsis as queries. Next step I would like to map reads to these contigs with hits. However, I don't know how to seive all the contigs with hits (nucleotide sequences) out after using tblastx since all sequences were translated in to amino acid sequences.
I tried "Toolbox-Classical Sequence Analysis-General Sequence Analysis-Extract sequence", but only amino acid sequences were obtained. I could also extract the nucleotide sequence of a single contig every time, but there are thousands of contigs with hits in my case.
Anyone knows how to achieve that?

GenoMax · 05-03-2016, 06:55 AM

@Yangan: Since your CLC license includes free tech support you may want to contact them about this question (I assume you want to do this within CLC). They may need to provide you with a plugin or custom code to do the action you are referring to.

Yangan · 05-03-2016, 07:39 AM

Quote:

Originally Posted by GenoMax

@Yangan: Since your CLC license includes free tech support you may want to contact them about this question (I assume you want to do this within CLC). They may need to provide you with a plugin or custom code to do the action you are referring to.

Thank you for your suggestion

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05-03-2016, 05:56 AM	#1
Yangan Junior Member Location: the Netherlands Join Date: Nov 2015 Posts: 2	How to extract nucleotide sequeces from tblastx table Hi there, I am a new learner of bioinformatics. I used Trinity to do de novo transcriptome assembly then imported the assembly.fasta file into CLC genomeworkbench 7.0.3 to run tblastx using this assembly file as local database while using all P450 cDNA of Arabidopsis as queries. Next step I would like to map reads to these contigs with hits. However, I don't know how to seive all the contigs with hits (nucleotide sequences) out after using tblastx since all sequences were translated in to amino acid sequences. I tried "Toolbox-Classical Sequence Analysis-General Sequence Analysis-Extract sequence", but only amino acid sequences were obtained. I could also extract the nucleotide sequence of a single contig every time, but there are thousands of contigs with hits in my case. Anyone knows how to achieve that?

05-03-2016, 06:55 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	@Yangan: Since your CLC license includes free tech support you may want to contact them about this question (I assume you want to do this within CLC). They may need to provide you with a plugin or custom code to do the action you are referring to.