I am working on molecular phylogeny in the order level. When I am extracting the sequences from NCBI Genebank, I found there are lot sequences marked as unverified. For concratenation of multiple genes, there are some sequences are missing or unverified in some species. May i take those for my phylogenetic analysis? Are there any problems in those sequences?
If there is no problem, then why those unverified sequences are present in NCBI Genebank??
I am quoting gene bank
"As part of the standard submission process, GenBank staff review submissions for biological accuracy and assist authors in providing accurate annotations. If GenBank staff is unable to verify the accuracy of the submitted sequences and/or annotations, they may now add a comment to the record stating that the sequence is unverified. Until the submitter is able to resolve the issues, such sequences will have the word ‘UNVERIFIED:’ at the beginning of their definition lines and will not be included in BLAST databases."
Shefali
I am quoting gene bank
"As part of the standard submission process, GenBank staff review submissions for biological accuracy and assist authors in providing accurate annotations. If GenBank staff is unable to verify the accuracy of the submitted sequences and/or annotations, they may now add a comment to the record stating that the sequence is unverified. Until the submitter is able to resolve the issues, such sequences will have the word ‘UNVERIFIED:’ at the beginning of their definition lines and will not be included in BLAST databases."
Shefali
Thank you Mam. That means I can not take those sequences for my phylogenetic analysis. Thank you Mam.
It depends. For example, if you submit a mitochondrial DNA sequence, call it "Shrew Cytb", but provide no specific information of which position corresponds to the beginning/end of your Cytb, then the sequence will be marked as unverified. What often happens is, you have a partial sequence of Cytb, so you don't fill in the annotation part of it because you think it's not needed. GenBank staff comes back to you asking for this info, but you can't be bothered to do it because your paper needs finalizing, and "why does it matter anyway?" kind of thinking. If that is the case, the sequence will probably be ok, but still marked as unverified.
However an alternative scenario is, someone submits a Cytb sequence will the correct information, but GenBank staff identified it ha a mutations that causes an early stop codon. Because biologically, early stop codons in Cytb will likely be lethal, GenBank staff will ask the author to carefully check the sequence for errors. Again, the author might choose not to chase this for various reasons, and the sequence gets marked as unverified.
So the short answer to your question is, if you are dealing with unverified sequences from Genbank, always best to make some data integrity checks yourself before using it. It also means you need to be careful if your phylogeny gives some strange and unexpected results. You might find that those strange and exciting results, involve sequences that are unverified.
Having said that, it's always a good idea to check GenBank sequences for data integrity. There was a very good paper on this a few years back in TREE: http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(03)00150-2. Obviously, the amount and diversity of data in Genbank has changed considerably since then, but the sentiment remains true.
Hope that helps.
Unverified means that sequence is not annotated. In this situation, sequence data might be ok but since it is not annotated and not compareable with previous accepted records, genebank stuff can not verify it. So, if there is no available verified sequence info for a certain organism in genebank, you can use unverified data in your analysis, but if there is verified one, that would be better.
Thanks everyone for your valuable suggestions. Unverified sequences are either not properly annotated or there are some stop codon related problems and they are not coming in the blast search.
The main issue is that after so much hard work, if those sequences are not coming in blast searches, then what are they stand for. How shall I check those sequences if there are not any published (verified) sequences of the same organism/species?
Is there a process to submit unannotated sequences if it is not similar to ref seq on blastn data base? Thanks
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