NCBIFetch

Keywords: NCBI, esearch, efetch, list

Retrieves records in the fasta format from a list of one or more unique identifiers.

Indroduction

The Perl script use an input file with al list of genes (ncbifetchn.pl) or proteins (ncbifetchp.pl).

The Entrez Programming Utilities esearch and efetch from the NCBI web site are used.

efetch

http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#toolparam

esearch

http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html

To manage a whole list the ncbi example perl script was modified.

The original script "eutils_example.pl" search only for one entry. See the original script

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_example.pl

We and with the help of a unknown programer modified the script, and this enable a search of a whole list of genes or proteins.

Example "input.txt" - proteins

Example "output.txt"

Manual (Windows Version)

1. Install perl
2. Open Comand Prompt
3. go to the folder with the perl script and input.txt.
   Perl script and input.txt in the same folder

4. Type the following command
   perl program input > output
   
   Nucleotide
   perl ncbifetchn.pl input.txt > output.txt
   Protein
   perl ncbifetchp.pl input.txt > output.txt

5. Open the result file output.txt

Remarks

• Close the text in the input.txt with a paragraph, otherwise the last entry will not be searched.
• The difference between ncbifetchp.pl and ncbifetchn.pl is only the script line
  $db = "protein";
  respectively
  $db = "Nucleotide";
• The script should also work on Linux or Mac OS
• You can change the format (default "fasta") in the line
  $report="fasta";

Downloads

ncbifetch.zip

Dieter Steinmetz (73228)