Hello, in January, I successfully used BLAST to find a homologue of HDV in a TSA dataset from a lizard. However, when I recently attempted to search for that sequence again, I couldn't find it in either TSA or SRA databases. Does anyone know why this might be the case? Any insights would be greatly appreciated. Thank you!
According to my knowledge It sounds like you're experiencing an issue with retrieving a sequence you previously identified in the Transcriptome Shotgun Assembly (TSA) or Sequence Read Archive (SRA) databases. There are several possible reasons why you might not be able to find the sequence now:Data Updates and Revisions:NCBI frequently updates its databases, and during such updates, certain sequences might be revised, reclassified, or even removed if they were found to be erroneous or redundant.Check if the TSA or SRA datasets have been updated or if there are new versions available.Sequence Relocation:Sometimes, sequences are reannotated and moved to different databases or given new accession numbers. It's possible that your sequence has been reclassified under a new ID.Try searching for the sequence using different identifiers or keywords.Database Removal or Privacy Settings:Occasionally, datasets are removed from public access due to various reasons, such as the submitter retracting the data or issues related to data privacy or quality.If the dataset was removed, there might be an associated notice or publication retraction.Search Parameters:Ensure that your BLAST search parameters are set correctly. Changes in the database or search settings might affect your ability to find the sequence.Double-check the search parameters, including the database you are querying, the search sensitivity, and the filters applied.Technical Issues:There might be temporary technical issues with the NCBI servers or your internet connection.Try accessing the databases from a different network or at a different time.Steps to Troubleshoot and Find the SequenceCheck Database Versions:Look for any recent updates or changes to the TSA or SRA databases. NCBI often provides release notes or updates about significant changes.Alternative Search Strategies:Use different BLAST programs (e.g., BLASTn, tBLASTn) and adjust the search parameters.Try using other related databases, such as GenBank, if the sequence might have been moved.Search Using Metadata:If you remember any specific metadata (e.g., sample ID, study title, organism details), use those to search the NCBI database or related publications.Contact NCBI Support:If you believe the sequence should still be available but cannot find it, consider reaching out to NCBI support for assistance. They can provide insights into any changes in the database that might affect your search.Explore Published Literature:If the sequence was part of a study, check the corresponding publication for any updates or supplementary data that might explain the sequence's current status.Use Archived Data:Check if you saved any local copies of the sequence or associated data when you first identified it. Having a copy can help you reference it accurately and potentially realign it with updated databases.
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