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Old 05-17-2012, 01:18 AM   #1
darren.obbard
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Location: Edinburgh, UK

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Default blastdbcmd question

Hi all,

Apologies that this isn't specifically nextgen.

Can anyone explain why I get two results with this query?

blastdbcmd -db nt -entry 94400888 -outfmt '%gi'
94400888i
78217416i

And is there anyway of using blastdbcmd -db nt -batch_entry that would guarantee a single result from each input line?

---FYI---
BLAST database client, version 2.2.26+

Thanks!

Darren
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Old 05-17-2012, 05:49 AM   #2
kmcarr
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You see two entries because the description line for gi|94400888 indicates that it is equivalent to gi|78217416. The NCBI nr and nt definition lines have a format convention which allows them to annotate equivalent entries. The BLAST tools understand this convention and can report that information. To see only the information for the primary gi you need to add '-target_only' to your blastdbcmd. Also the -outfmt is '%g' not '%gi'. The extra 'i' is simply being added to the end of the gi string as shown in your output.
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Old 05-17-2012, 06:03 AM   #3
darren.obbard
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Great! Thank you so much - made my day much better....

('%gi' -oops! this was a wild guess, that /nearly/ worked, and I didn't think it through or look it up)
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