I have list of accession and GI no. Now I want publication associated with sequence. list is long at least 3000 entry .Manually it will take long time. So is there any tool or software or search engine retrieve literature from accession or Gi automatically?
If you are working with protein sequences, retrieve uniprot id then its relevant publications in uniprot database
Definately saravanan sir, I have both.but problem is large no of entry. Manually it wil take more time. Problem is large no. of entry.
Gopal,
When u visit UniProt website, u can find retreive tab where u can submit all uniprot accession number to retrieve data, Uniprot will list them.
u can customize the view of results to display pubmed it which can be saved as tab-delimited file.
Hope it helps
Dears,
query is about how to find out all publications related to accession numbers by a single click, so i think there is no software to do that you can go manually.be happy
Saravanan SIr, I have nucleotide sequence so and i want publication by oneclick where this sequence can be dowmloaded or visulize at onece. It wil be suitable for annonation of large sequence data.
if its a nucleotide sequence, i would prefer to access thru ncbi nucleotide database itself. Check out the The E-utility Web Service (SOAP).
Check out this link: http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.Application_3_Retrieving_large
sample PERL scripts to access large dataset would be helpful for you.
Saravanan SIr, Till you are not getting my issue. My issue is to find all literature related to sequence not a sequence. Sequence data very easy to get but literature in which it is included. It is easy for one sequence by just seeing genebank format but If any remedies there even give only title of publication then it will be far more helpful. and save lots of time. Manually I have already started.
What database are you using. If this is GenBank, then there is no way to pull references from a list of accession straight into a program like EndNote. However, you can export all of the information in one batch by selecting them all, hitting the "Send To" button at the bottom, "File" and "GenBank Full" format. This will give you a file that has all of the citation in it along side the sequences and I'm sure it wouldn't be hard to write a Perl script or something to pull these out and compile them (I don't know of one that already exists that I can point you to, sorry). Please post back if you figure out an easier way. Good luck!
Thanks Michael Green, Yes I had already done it. But What I dont know much about Perl and it's use. I will learn to use Perl for fetching information. Problem is that I am from Bio science back ground lacking very basic knowledge about computing language and I have limited time about 45 day to accomplish my work. So I am looking for remedies first. But If you know best way to learning computing language withing short time then please let me inform. Currently I am try to get connected with IT technician or Bioinformatics master. If you know person good in this thing then please let me inform. Thank you again.
I can write php code for getting all the references from any number of NCBI GI accessions. Remind you again only GI IDs.
Dear Ravi Kanth Reddy Sathi.Can you please pass on this. If you have published on web then may I have Webaddress?
Give me half an hour I will make an online tool and post the link here...
Here is the link... took one hour...
http://tools.srkrlab.com/litretriever/
http://tools.srkrlab.com/litretriever/
I created the tool today itself. But forget to upload the file containing a custom function created by me. So it didn't work initially. Now I have corrected it too. So it should be working fine.
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