AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

Nucleic Acids Research
Alan MedlarLiisa Holm

Abstract

We present AAI-profiler, a web server for exploratory analysis and quality control in comparative genomics. AAI-profiler summarizes proteome-wide sequence search results to identify novel species, assess the need for taxonomic reclassification and detect multi-isolate and contaminated samples. AAI-profiler visualises results using a scatterplot that shows the Average Amino-acid Identity (AAI) from the query proteome to all similar species in the sequence database. Taxonomic groups are indicated by colour and marker styles, making outliers easy to spot. AAI-profiler uses SANSparallel to perform high-performance homology searches, making proteome-wide analysis possible. We demonstrate the efficacy of AAI-profiler in the discovery of a close relationship between two bacterial symbionts of an omnivorous pirate bug (Orius) and a thrip (Frankliniella occidentalis), an important pest in agriculture. The symbionts represent novel species within the genus Rosenbergiella so far described only in floral nectar. AAI-profiler is easy to use, the analysis presented only required two mouse clicks and was completed in a few minutes. AAI-profiler is available at http://ekhidna2.biocenter.helsinki.fi/AAI.

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Citations

Jul 6, 2019·International Journal of Systematic and Evolutionary Microbiology·Biao TangXiaoming Ding
Feb 19, 2020·International Journal of Systematic and Evolutionary Microbiology·Dmitriy V VolokhovLaszlo Stipkovits
Jun 26, 2020·International Journal of Systematic and Evolutionary Microbiology·Maximilian FlaizFrank R Bengelsdorf
Apr 29, 2020·Phytopathology·Olufemi A Akinsanmi, Lilia C Carvalhais
Jul 14, 2020·International Journal of Systematic and Evolutionary Microbiology·Timofey A PankratovAleksandr A Ashikhmin
Jul 14, 2020·Genome Biology and Evolution·Jacqueline HollensteinerRolf Daniel
Jun 1, 2019·Critical Reviews in Microbiology·Fernando Hayashi Sant'AnnaLuciane M P Passaglia
Sep 5, 2020·International Journal of Systematic and Evolutionary Microbiology·Jin-Soo SonSa-Youl Ghim
Mar 29, 2020·Microbiology Resource Announcements·Sarah J KennedyLindsey N Shaw
May 11, 2019·Microbiology Resource Announcements·Michael J ZillioxCatherine Putonti
Jul 8, 2019·Current Microbiology·Anwesha Ghosh, Punyasloke Bhadury
Aug 14, 2020·International Journal of Systematic and Evolutionary Microbiology·Feilong ChenShaoxing Chen
Aug 2, 2018·BMC Bioinformatics·Alan Medlar, Liisa Holm
Aug 12, 2019·Antonie van Leeuwenhoek·Siqi SunShaoxing Chen
Apr 1, 2020·International Journal of Systematic and Evolutionary Microbiology·Dmitriy V VolokhovTobias Eisenberg
Oct 10, 2020·International Journal of Systematic and Evolutionary Microbiology·Xiaoxiao HouYan Gao
Oct 10, 2020·International Journal of Systematic and Evolutionary Microbiology·María Paula Parada-PinillaSandra Baena
Nov 4, 2020·International Journal of Systematic and Evolutionary Microbiology·Jiajie ZhangZong-Jun Du
Nov 12, 2020·Journal, Genetic Engineering & Biotechnology·Lateef Babatunde Salam, Oluwafemi Sunday Obayori
Dec 5, 2020·International Journal of Systematic and Evolutionary Microbiology·Xiaoxiao HouZhiwei Chen
Jan 6, 2021·Archives of Microbiology·Kannan Asha, Punyasloke Bhadury
Apr 22, 2021·Antonie van Leeuwenhoek·Daniele Bussioli Alves CorrêaSuzete Aparecida Lanza Destéfano
Apr 29, 2021·International Journal of Systematic and Evolutionary Microbiology·Huda MahmoudLiny Jose
May 7, 2021·International Journal of Systematic and Evolutionary Microbiology·Vincent PetaHeike Bücking
Apr 24, 2021·Microbiology Resource Announcements·Austin HerbertWilliam Turechek
Sep 26, 2021·Protein Science : a Publication of the Protein Society·Petri Törönen, Liisa Holm
Sep 9, 2021·Applied and Environmental Microbiology·Sarah J KennedyLindsey N Shaw
Nov 6, 2021·Scientific Reports·Isabelle Q PhanPeter J Myler

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