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Old 01-24-2013, 06:18 PM   #1
Tsuyoshi
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Location: japan

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Default Problem with batch entrez

HI ALL!
Here is a very basic question, however, I have been frustrated by it.
I got a set of protein GI numbers, and I upload it to the Batch entrez tool in the website of NCBI (http://www.ncbi.nlm.nih.gov/sites/batchentrez) to output the fasta format data for each protein. Previously it worked well, however, recently , the output file was empty but a single sentence "Your session has expired. Please repeat your search." I have tried for many times but it repeats the error.
Does anyone know what is wrong with the batch entrez tool? Or is there any available simple way to retrieve the fasta proteins? Thanks!
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Old 01-25-2013, 02:45 PM   #2
maubp
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How many sequences was this for? And what time of day - avoid USA working hours as that is when Entrez is most busy.
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Old 01-25-2013, 03:01 PM   #3
Richard Finney
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I've found batch entrez to be extremely unreliable.
The NCBI tool idfetch is pretty good.
Also , see response from Michael Schubert here :
http://www.biostars.org/p/7166/ ...

This you can then use to EFetch/ESummary your results
http://www.ncbi.nlm.nih.gov/entrez/e...2494,325152492
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Old 01-25-2013, 10:28 PM   #4
Tsuyoshi
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Default

Quote:
Originally Posted by maubp View Post
How many sequences was this for? And what time of day - avoid USA working hours as that is when Entrez is most busy.
Thank you maubp!
I have tried to input the sequences from 10 to 100, and in different times, and the error occurred again and again. Therefore, I found an alternative way to get the famat sequences directly using website.

Please find the description here http://edwards.sdsu.edu/labsite/inde...d-using-entrez
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Old 01-25-2013, 10:30 PM   #5
Tsuyoshi
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Location: japan

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Quote:
Originally Posted by Richard Finney View Post
I've found batch entrez to be extremely unreliable.
The NCBI tool idfetch is pretty good.
Also , see response from Michael Schubert here :
http://www.biostars.org/p/7166/ ...

This you can then use to EFetch/ESummary your results
http://www.ncbi.nlm.nih.gov/entrez/e...2494,325152492
Thank you Richard!
I found another way to get the sequences. Please find the descriptions here
http://edwards.sdsu.edu/labsite/inde...d-using-entrez
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Old 01-24-2018, 01:12 AM   #6
netazuck
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Default solution to "problem with batch entrez" that worked for me

open a different tab on your browser for NCBI nucleotide search (https://www.ncbi.nlm.nih.gov/nuccore/), click on "advanced" below the search bar, and click on "clear history" under the "history" section (where you'll see all your previous searches). This worked for me!
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