18rRNA gene DNA sequences- coding or non coding for alignment? · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

18rRNA gene DNA sequences- coding or non coding for alignment?

I have DNA sequences I acquired from amplification of the 18S rRNA gene of parasite DNA in insects. I am trying to understand the sequencing alignment process as I have all sequences in MEGA with blast matches. For alignment, is this DNA protein coding or not? I was under impression it does not code for protein, only transcribed to RNA. Given options of Align DNA only, or align codons (coding for protein) which is most appropriate? Thanks for helping!

gene sequence

• 2,100 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by flowerchild4 •

1 answer

You are right, ribosomal RNA doesn't code for protein, therefore only nucleotide level alignments make sense.

• 0 views • link

updated 3.6 years ago by Ram

• written 11.2 years ago by Michael Dondrup

Log in to answer this question.

More posts like this

Aligning sequences with multiple genetic codes!
written 2.7 years ago by George X. •

Hello everyone! I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic …
Reading frame after aligning DNA for codeml analysis
written 3.0 years ago by sodiumnitrate •

I have a bunch of protein-coding DNA sequences in the correct reading frame, such that upon translation, I get the protein sequences. If I align …
Most efficient command line tool for translating the DNA sequences into Protein ?
written 4.3 years ago by sunnykevin97

Hi, What is the most efficient tool for translating the DNA sequences into protein? And remove the stop codons more robustly. I tried **TranslatorX**, it …
Difference between NCBI and mega 6 software based nucleotide sequence alignments
written 5.0 years ago by ashenafymamo •

I tried to align two nucleotide sequences using NCBI "blast" with "Align two or more sequences" program and Mega 6 software . The results of …
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
written 7.8 years ago by contact •

This article shows what 16S/18S/ITS amplicon sequencing is and how it works. Let’s get ready to learn. 16S/18S/ITS amplification sequencing uses the next/third generation sequencing …
Multiple Sequence Alignment for tree building Advice
written 11.2 years ago by flowerchild4 •

Hi All, **Background**: I am trying to build a tree of sequences (non-coding DNA) I obtained in my lab, along with appropriate similarly related known …
Most suitable alignment program for Ka/Ks analysis of whole genome coding sequences
written 12.0 years ago by Cytosine

Hi, I've been trying to get Ka/Ks scores of genome-wide pairwise alignments of coding sequences from two strains of the same organism. (i.e. very high …
Solving Stop Codons
written 13.8 years ago by lmumladze •

<p>Hi I have D-loop CO1 sequences gained from automated sequencer. I export abi fails to fasta format and then import in MEGA to align and …
Stop Codons In Mega 5 Multiple Alignment With Muscle...
written 14.5 years ago by Winawer •

<p>Hello,</p> <p>I'm pretty new to the bioinformatics space, so forgive the newbishness of the question. :-) I'm trying to do a multiple alignment of coding …
Multiple Sequence Alignment For Cdnas
written 15.9 years ago by Haibao Tang

<p>Now I have a collection of sequences that are derived from cDNAs, but most of them are partial. I can start aligning them, but I'd …