PaperBLAST – Find papers about a protein or its homologs

 


Enter a sequence in FASTA or Uniprot format:

Or see example results for the putative alcohol dehydrogenase WP_012018426.1, which is actually the regulator ercA.

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, Swiss-Prot, and EcoCyc. As of March 2017, PaperBLAST links over 360,000 different protein sequences to over 700,000 articles. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access.

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

We also use manually-curated links between protein sequences and articles. We index proteins from NCBI's RefSeq if a GeneRIF entries links the gene to an article in PubMed®. GeneRIF also provides a short summary of the article's claim about the protein, which we provide instead of a snippet. We index proteins from Swiss-Prot (the curated part of UniProt) if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). And we index every protein EcoCyc, a curated database of the proteins in Escherichia coli K-12. For the entries from Swiss-Prot and EcoCyc, we provide a short curated description of the protein's function. Most of these entries also link to articles in PubMed.

The code for PaperBLAST is available here.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory