Evidence map›Paper›PMID 31411700›Full record

ArticleMolecular biology and evolution2019

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.

Anurag Priyam, Ben J Woodcroft, Vivek Rai, Ismail Moghul, Alekhya Munagala, Filip Ter, Hiten Chowdhary, Iwo Pieniak, Lawrence J Maynard, Mark Anthony Gibbins and 12 more

Abstract readEvaluation Study
In one paragraph

Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 218 papers.

0numbers the graph read from it
0cells of the map it votes in
218citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

218 citing papers in PubMed.

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  19. Structures ofScience advances · 2026
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158 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Anurag PriyamSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Ben J WoodcroftSchool of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia.
Vivek RaiDepartment of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India.
Ismail MoghulSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Alekhya MunagalaDepartment of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, India.
Filip TerSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Hiten ChowdharyDepartment of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, India.
Iwo PieniakSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Lawrence J MaynardSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Mark Anthony GibbinsDepartment of Computer Science, Royal Holloway University of London, Surrey, United Kingdom.
HongKee MoonScientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
Austin Davis-RichardsonSan Francisco, CA.
Mahmut UludagComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
Nathan S Watson-HaighBioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, Australia.
Richard ChallisInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
Hiroyuki NakamuraSpiber Inc, Kakuganji Tsuruoka, Yamagata, Japan.
Emeline FavreauSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Esteban A GómezSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
Tomás PluskalWhitehead Institute for Biomedical Research, Cambridge, MA.
Guy LeonardLiving Systems Institute, University of Exeter, Exeter, United Kingdom.
Wolfgang RumpfThe Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH.
Yannick WurmSchool of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

Funding

Biotechnology and Biological Sciences Research Council BB/K004204/1
6 · The paper itself

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.

Indexed as

Genetic TechniquesSoftwareComputational BiologyBLASTcomparative genomicssequence analysisvisualization

Identifiers

PMID31411700
PMCPMC6878946

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.