Evidence map›Paper›PMID 32683444›Full record

ArticleBioinformatics (Oxford, England)2021

Machine Boss: rapid prototyping of bioinformatic automata.

Jordi Silvestre-Ryan, Yujie Wang, Mehak Sharma, Stephen Lin, Yolanda Shen, Shihab Dider, Ian Holmes

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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.

Jordi Silvestre-RyanDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Yujie WangDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Mehak SharmaDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Stephen LinDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Yolanda ShenDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Shihab DiderDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.
Ian HolmesDepartment of Bioengineering, University of California, Berkeley, CA 94720, USA.

Funding

GENOMICST32HG000047 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI RASMUS NIELSEN, Daniel Soleyman Rokhsar · 2000 to 2026
$13.5M
Web-based visualization of coronavirus genomes and proteinsR01HG004483 · NHGRI · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$9.3M
Novel Web-based Tools for Collaborative Community-Driven Genome Feature AnnotatioR01GM080203 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Ian H Holmes · 2007 to 2026
$8.5M
Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics DataU24CA220441 · NCI · UNIVERSITY OF CALIFORNIA BERKELEY · PI HOLMES, IAN H, STEIN, LINCOLN D. · 2017 to 2020
$2.7M
NCI NIH HHS U24 CA220441NHGRI NIH HHS R01 HG004483NHGRI NIH HHS T32 HG000047NIGMS NIH HHS R01 GM080203
6 · The paper itself

Abstract

motivationMany software libraries for using Hidden Markov Models in bioinformatics focus on inference tasks, such as likelihood calculation, parameter-fitting and alignment. However, construction of the state machines can be a laborious task, automation of which would be time-saving and less error-prone.

resultsWe present Machine Boss, a software tool implementing not just inference and parameter-fitting algorithms, but also a set of operations for manipulating and combining automata. The aim is to make prototyping of bioinformatics HMMs as quick and easy as the construction of regular expressions, with one-line 'recipes' for many common applications. We report data from several illustrative examples involving protein-to-DNA alignment, DNA data storage and nanopore sequence analysis. AVAILABILITY AND IMPLEMENTATION: Machine Boss is released under the BSD-3 open source license and is available from http://machineboss.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Computational BiologySoftwareAlgorithmsInformation Storage and RetrievalSequence Analysis

Identifiers

PMID32683444
PMCPMC8034524

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Registered trials

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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.