Question: Can I Parse Out The Refseq Entries That Are Unplaced Or Provisional?
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7.6 years ago by
random2607820 wrote:

I am trying to find a way to exclude the unplaced contigs and provisional RefSeq entries from my local copy of the RefSeq database. I am not sure how to do this. I tried using blastdbcmd but there is no way to search for a string that is not part of the sequence identifier. I tried to find all RefSeq entries at NCBI with the word 'provisional' in them but got a bunch that do not have the word 'provisional' in them.

I was able to get a list of gi numbers for all RefSeq entries that have the words 'unplaced genomic contig' in the entry header.

Any ideas on getting the sequences labelled as provisional?

Thank you.

refseq contigs parsing • 1.5k views
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