Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Author:

Priyam Anurag1,Woodcroft Ben J2,Rai Vivek3,Moghul Ismail1,Munagala Alekhya4,Ter Filip1,Chowdhary Hiten4,Pieniak Iwo1,Maynard Lawrence J1,Gibbins Mark Anthony5,Moon HongKee6,Davis-Richardson Austin7,Uludag Mahmut8,Watson-Haigh Nathan S9,Challis Richard1011ORCID,Nakamura Hiroyuki12,Favreau Emeline1ORCID,Gómez Esteban A1,Pluskal Tomás13ORCID,Leonard Guy14ORCID,Rumpf Wolfgang15,Wurm Yannick116ORCID

Affiliation:

1. School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom

2. School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia

3. Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India

4. Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, India

5. Department of Computer Science, Royal Holloway University of London, Surrey, United Kingdom

6. Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

7. San Francisco, CA

8. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia

9. Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, Australia

10. Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA

11. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

12. Spiber Inc, Kakuganji Tsuruoka, Yamagata, Japan

13. Whitehead Institute for Biomedical Research, Cambridge, MA

14. Living Systems Institute, University of Exeter, Exeter, United Kingdom

15. The Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH

16. 5Bases Limited, London, United Kingdom

Abstract

Abstract Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

Funder

European Research Council

United States Department of Energy

Biotechnology and Biological Sciences Research Council

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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