How can we check the purity of the gene sequence (in percent)? Is there any software or online tool or any calculation?
As far as I know there is no tool to check the "purity" of a sequence read. I guess this question is the follow up to this one:
https://www.researchgate.net/post/How_to_check_the_chromatogram_of_16S_rDNA_sequence
That thread leaves open a number of important questions like: Is your sequence from an unculturable bacterium? Is it from a "raw" PCR product or from a product cloned into some vector?
One could come up with some kind of measure by, e.g. performing base-calling with phred and then checking the phred score for each base in relation to the scores of its neighbours. But the central questions is: What do you need that information for? I have never heard of the term "purity of the sequence" before...
Is this sequence is newly assembled and you are checking for sequencing error?
If this is the case,then align the SSU-rRNA for that organism with your new sequence. If it is not 100% identical then either there is sequencing error or sequence is different.
Hi, if you already sequenced your gene then you can check the electrophoretogram. Cheers, Nadine
what type of purity you need to check, why don't you try the alignment software from NCBI.
Dr. Deepak
I want to check the purity of sequence i.e. how much pure or good is the sequence (in percent). I think the alignment of the sequence does not give purity of the sequence instead it gives similarity with other sequences.
for example: if I need to check the similarity of my unknown sequence then in NCBI it gives some % similarity with known bacterial sequence.
Am I right? If not, please correct me as I am not much familiar with these.
Also, I would be highly thankful to you If you please guide me in this.
Thanks,
As far as I know there is no tool to check the "purity" of a sequence read. I guess this question is the follow up to this one:
https://www.researchgate.net/post/How_to_check_the_chromatogram_of_16S_rDNA_sequence
That thread leaves open a number of important questions like: Is your sequence from an unculturable bacterium? Is it from a "raw" PCR product or from a product cloned into some vector?
One could come up with some kind of measure by, e.g. performing base-calling with phred and then checking the phred score for each base in relation to the scores of its neighbours. But the central questions is: What do you need that information for? I have never heard of the term "purity of the sequence" before...
Hello Kunal,
I am agree with @Christian. I never heard about purity of sequences in bioinformatics as well. May be there are some techniques in wet lab which can help.
Dear Kunal Garg,
The purity check and concentration of DNA is important for good signal sequencing. If you want check % identity of your sequence, you can use blastn.
Hello Kunal,
Albeit, I am in agreement of all the comments made above. However, i would suggest you to consult help-disk at the NCBI site. They may better guide you provided you need additional information other than blast tools. Good luck.
Some ideas on how to examine sequences for quality and reliability are presented here:
https://www.researchgate.net/publication/235931750_Five_simple_guidelines_for_establishing_basic_authenticity_and_reliability_of_newly_generated_fungal_ITS_sequences
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers
Article Five simple guidelines for establishing basic authenticity a...
Article Incorporating molecular data in fungal systematics: A guide ...
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