Seek & Blastn

Seek for nucleotide sequences in pdf files and then call a local version of blastn.
To try the prototype: select a zip file containing pdf files... upload and wait... wait... for a link to results.

Please consider having a look at how to interpret results.

The seek& blastn version is in testing phase and may therefore produce false-positive and false-negative results.
Seek & blastn searches query nucleotide sequences against the human genomic + transcript database. Published nucleotide sequence reagents from other species may therefore be incorrectly identified by seek & blastn.
We strongly recommend that Seek&Blastn results be subjected to manual checking prior to taking any further action, such as contacting authors or journal editors, or flagging publications using PubPeer or social media.

Any comments:
Jennifer Byrne
Guillaume Cabanac
Bertrand Favier
Thierry Gautier
Cyril Labbe

If you would like to support the further development of Seek&Blastn, please contact Cyril or Jennifer.
More in:
Fact Checking Nucleotide Sequences in Life Science Publications: The Seek & Blastn Tool
Slides

The problematic papers flagged by Seek&Blastn and reported in the following articles are tabulated at the PPP:

📝 Park, Y., West, R.A., Pathmendra, P., Favier, B., Stoeger, T., Capes-Davis, A., Cabanac, G., Labbé, C., Byrne, J.A. (2022).
Identification of human gene research articles with wrongly identified nucleotide sequences.
Life Science Alliance. https://doi.org/10.26508/lsa.202101203, 5(4), e202101203.
▷ Featured in Nature (Else, 2022)

📝 Byrne, J.A., Park, Y., West, R.A., Capes-Davis, A., Favier, B., Cabanac, G., Labbé, C. (2021).
The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications.
Scientometrics. https://doi.org/10.1007/s11192-021-03871-9, 126(4), 3513–3534.

📝 Labbé, C., Cabanac, G., West, R.A., Gauthier, T., Favier, B., Byrne, J.A. (2020).
Flagging incorrect nucleotide sequence reagents in biomedical papers: To what extent does the leading publication format impede automatic error detection?
Scientometrics. https://doi.org/10.1007/s11192-020-03463-z, 124(2), 1139–1156.

📝 Labbé, C., Grima, N., Gauthier, T., Favier, B., Byrne, J.A. (2019).
Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool.
PLoS ONE. https://doi.org/10.1371/journal.pone.0213266, 14(3), e0213266.

📝 Byrne, J.A., Labbé, C. (2017).
Striking similarities between publications from China describing single gene knockdown experiments in human cancer cell lines.
Scientometrics. https://doi.org/10.1007/s11192-016-2209-6, 110(3), 1471–1493.