getting bulk fasta by Batch Entrez

Question

[zizigolu]

Hi friends,

I have some genebank necleotide accession and I want to get their fasta from Batch Entrez but just one (NM_001288905.1) was the result, how possible please?

batch entrez input

XM_006486085
XM_006467849
XM_006479293
XM_006466969
XM_006469634
XM_006469633
XM_006469632
XM_006469635
XM_006475025
XM_006475026
XM_006475028
XM_006475027
XM_006475024
XM_006464699
XM_006464700
XM_006464698
XM_006475334
XM_006476712
XR_370393
XR_370394
XR_370392
XM_006464709

batch entrez out put

Received lines: 22
Rejected lines: 0
Removed duplicates: 0
Passed to Entrez: 22
Retrieve records for 22 UID(s) (a link)

Answer 1

[anp375]

I have never seen accession numbers like that before. Do you have a link that explains them? Are you using a Mac? Mac text files use \r instead of \n to signify new lines so maybe its not recognizing individual accession numbers. Did you try them individually to see if you get the same result?

[zizigolu]

I am in windows, I had a list of gene symbols like LOC102627810 that converted them to genbank nucleotide accession by bioDBnet by this link (http://biodbnet.abcc.ncifcrf.gov/db/db2db.php) then I copied the result (for example XM_006469893) in notepad as an input for Batch Entrez but I got just one output (NM_001288905.1). When I search the result one by one I saw the result is different, now how I can get the bulk result because one by one taking too long time

Thank you

[zizigolu]

Hey Sarah instead of genbank nucleotide accession you should select genbank nucleotide GI in bioDBnet, then:

• Create a file with a list of GI or accession numbers and save it locally
• Select the database from which the list of accessions or UIDs originated
• Use the 'Browse' button to select the filename containing the list of UIDs from your system directory
• Press the Retrieve button and you will see a list of document summaries
• Select a format in which to display the data for viewing, and/or saving
• Select 'Send to file' to save the file.

Hope this helps!