What’s your problem? Open Thread
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.
So What’s Your Problem? And What’s Your Solution? 
You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.
Hi there, i have problems with my sequence that i try to submit to the genbank and i couldn’t find the solution/ don’t know how to solve it. Further information as below:
“While processing your GenBank submissions GU591702-GU591721, we have come across an issue that requires your attention.
When appropriate, annotating an open reading frame on a sequence
with a coding region span is informative. Therefore, based
on the information you have supplied and on BLAST similarity search
results, we have added the coding regions shown in the appended
records.
However, internal stop codons have been detected in the conceptual
translation of the following coding regions:
xxxxxx
Additionally, the following coding regions do not appear to contain valid
start codons:
xxxxxxx
Appended is an alignment of your sequences indicating possible frameshifts
in the sequences as noted above. Additionally, you will notice that the
3′ ends of your sequences appear to show very little similarity. This
is an indication that the 3′ ends may contain regions of low quality sequence.
Therefore, please remove any potential low quality sequence from the
ends of your sequences”.
I really appreciate if anyone can help me to solve this problems.
Thank you in advance.
Good morning nurdalila–
I assume you mean you are submitting to deposit the sequence in Genbank, with Sequin ( http://www.ncbi.nlm.nih.gov/projects/Sequin/ ) ?
I haven’t done this in a while, so I don’t know what the output looks like at this point. But it sounds to me like there’s a conflict between what you may have indicated your sequence is (an ORF) and their automated assessment of that ORF. So it may be that it’s an annotation problem. Maybe you aren’t submitting an ORF?
It seems to me that this could also be a way of telling your that there is an issue with the sequence quality. If your believe it to be coding for a protein and they can’t find the ORF, they are trying to tell you to re-examine the sequence?
You might look through the Sequin documentation to see if there is something else that stands out: http://www.ncbi.nlm.nih.gov/projects/Sequin/QuickGuide/sequin.htm#before
If nothing seems to amiss, you should probably work with the NCBI help desk folks on that (the link at the bottom of the sequin page).