Question: Partial Cds Extraction From Incomplete Transcripts
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gravatar for Raghul
7.2 years ago by
Raghul200
Italy
Raghul200 wrote:

Hi to all, I have 454 RNA transcripts assembled into Isotigs using Newbler. They are complete, they miss 5' end, they miss 3' end and sometimes they miss both (as revealed by blastx). I want only the CDS (coding sequence) because I want to check the propensity of GC (only in CDS) & hydrophilic amino acids (after translation) in my transcriptome. So do you guys know any tool which does this? So all kind of suggestions are welcome!

thank u raghul

cds extraction rna • 2.7k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 7.2 years ago by Raghul200
2

Just to note that by definition, an incomplete transcript cannot yield a CDS. I suppose it can yield a "partial CDS".

ADD REPLYlink written 7.2 years ago by Neilfws48k

I am having the assembled transcripts.

ADD REPLYlink written 7.2 years ago by Raghul200

Thanks to all for answering the questions. I think for protein sequence analysis, I can use OrfPredictor. It takes sequences & blastx output for analysis & give predicted peptide sequences in the FASTA formatI am looking ways to identify (partial)CDS in RNA. This answer was available for another question in Biostar forum for a different question.

ADD REPLYlink written 7.2 years ago by Raghul200

Thanks to all for answering the questions. I think for protein sequence analysis, I can use OrfPredictor. It takes sequences & blastx output for analysis & give predicted peptide sequences in the FASTA format. Now I am looking ways to identify (partial)CDS in RNA. This answer was available for another question in Biostar forum for a different question.

ADD REPLYlink written 7.2 years ago by Raghul200
1
gravatar for Damian Kao
7.2 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

You'll probably want to find the longest ORF and take that as the CDS. You can do a six frame translation and find the longest ORF. Since you might be missing 5' or 3' or both, remember to account for missing stop or start codons.

ADD COMMENTlink written 7.2 years ago by Damian Kao15k

The problem here is even after assembled into contigs, many are missing 3 or 5 ends. But still such analysis can be done because no other information is available for this protozoa.

ADD REPLYlink written 7.2 years ago by Raghul200

raghul, I think there is not much more you can do about ORFs. use getORFs to find the longest ORF. If the stop codon is missing you will not get the right frame in any case using getORF.

ADD REPLYlink written 7.2 years ago by Michael Dondrup45k
1
gravatar for Michael Dondrup
7.2 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

The standard approach for this would be to run a gene prediction software like Glimmer, GeneMark, or Critica on your contigs. Also, try to run a tBLASTx search.

ADD COMMENTlink written 7.2 years ago by Michael Dondrup45k
1
gravatar for Jack Min
7.1 years ago by
Jack Min10
Jack Min10 wrote:

You can write a perl script to extract cds region from your input sequences using the information produced by OrfPredictor as in the definition lines of the output containing the frame value, the start and the end position of the cds.

ADD COMMENTlink written 7.1 years ago by Jack Min10
1

I added a function to the OrfPredictor server to generate the CDS file. Please try it out.
Jack Min

ADD REPLYlink written 7.1 years ago by Jack Min10

the server is available at http://proteomics.ysu.edu/tools/OrfPredictor.html

ADD REPLYlink written 7.1 years ago by Jack Min10
0
gravatar for Chris Miller
7.2 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Are these already aligned? If, so you could use bedtools to intersect a bed file containing your coding regions with your bam file:

intersectBed -abam yourbamfile.bam -b cdsfile.bed
ADD COMMENTlink written 7.2 years ago by Chris Miller20k

Yes it is already assembled into contigs & it is a protozoa. It has no complete genome sequence available.

ADD REPLYlink written 7.2 years ago by Raghul200
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