Evidence map›Paper›PMID 28293277›Full record

ArticleAlgorithms for molecular biology : AMB2017

On avoided words, absent words, and their application to biological sequence analysis.

Yannis Almirantis, Panagiotis Charalampopoulos, Jia Gao, Costas S Iliopoulos, Manal Mohamed, Solon P Pissis, Dimitris Polychronopoulos

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Algorithms for molecular biology : AMB, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Zimin patterns in genomes.PLoS computational biology · 2026
    Article
  2. The fitness cost of spurious phosphorylation.bioRxiv : the preprint server for biology · 2023
    Article
  3. Article
  4. Evolutionary selection against short nucleotide sequences in viruses and their related hosts.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020
    Article
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

7 authors.

Yannis AlmirantisNational Center for Scientific Research Demokritos, Neapoleos, 153 10 Athens, Greece.
Panagiotis CharalampopoulosDepartment of Informatics, King's College London, The Strand, London, WC2R 2LS UK.
Jia GaoDepartment of Informatics, King's College London, The Strand, London, WC2R 2LS UK.
Costas S IliopoulosDepartment of Informatics, King's College London, The Strand, London, WC2R 2LS UK.
Manal MohamedDepartment of Informatics, King's College London, The Strand, London, WC2R 2LS UK.
Solon P PissisDepartment of Informatics, King's College London, The Strand, London, WC2R 2LS UK.
Dimitris PolychronopoulosComputational Regulatory Genomics, MRC Clinical Sciences Centre (CSC), Du Cane Road, London, W12 0NN UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe deviation of the observed frequency of a word

resultsIn this article, we propose an [Formula: see text]-time and [Formula: see text]-space algorithm to compute all [Formula: see text]-avoided words of length

conclusionsThe systematic search for avoided words is particularly useful for biological sequence analysis. We present a linear-time and linear-space algorithm for the computation of avoided words of length

Indexed as

Absent wordsAvoided wordsConserved non-coding elementsSuffix treeUltraconserved elementsUnderrepresented words

Identifiers

PMID28293277
PMCPMC5348888

What OpenQuestion holds

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LicenceCC BY
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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.