ConsensusPrime - A Bioinformatic Pipeline For Ideal Consensus Primer Design Article Swipe
Maximilian Collatz
,
Sascha D. Braun
,
Stefan Monecke
,
Ralf Ehricht
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1030641/v1
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.21203/rs.3.rs-1030641/v1
High quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. The identification of homogeneous regions in alignments can be done manually only if alignments are small and if they contain sequences of high similarity. For large and inhomogeneous alignments, the process of finding the best regions needs to be automated.The ConsensusPrime pipeline was developed to detect the most homolog regions from multiple sequences. It automates the prediction of optimal consensus primers for analytical and diagnostic procedures/assays.ConsensusPrime is a fast and easy to use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and webservices. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are freely available on GitHub (https://github.com/mcollatz/ConsensusPrime).
Related Topics
Concepts
Executable
Computer science
Pipeline (software)
Consensus sequence
Source code
Data mining
Identification (biology)
Code (set theory)
Similarity (geometry)
Computational biology
Programming language
Artificial intelligence
Base sequence
DNA
Biology
Genetics
Image (mathematics)
Set (abstract data type)
Botany
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.21203/rs.3.rs-1030641/v1
- https://www.researchsquare.com/article/rs-1030641/latest.pdf
- OA Status
- green
- Cited By
- 1
- References
- 4
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3211046449
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3211046449Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.21203/rs.3.rs-1030641/v1Digital Object Identifier
- Title
-
ConsensusPrime - A Bioinformatic Pipeline For Ideal Consensus Primer DesignWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-11-02Full publication date if available
- Authors
-
Maximilian Collatz, Sascha D. Braun, Stefan Monecke, Ralf EhrichtList of authors in order
- Landing page
-
https://doi.org/10.21203/rs.3.rs-1030641/v1Publisher landing page
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https://www.researchsquare.com/article/rs-1030641/latest.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://www.researchsquare.com/article/rs-1030641/latest.pdfDirect OA link when available
- Concepts
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Executable, Computer science, Pipeline (software), Consensus sequence, Source code, Data mining, Identification (biology), Code (set theory), Similarity (geometry), Computational biology, Programming language, Artificial intelligence, Base sequence, DNA, Biology, Genetics, Image (mathematics), Set (abstract data type), BotanyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
-
2023: 1Per-year citation counts (last 5 years)
- References (count)
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4Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W2137015675, https://openalex.org/W2162098634, https://openalex.org/W2792034759, https://openalex.org/W2039146500 |
| referenced_works_count | 4 |
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| corresponding_author_ids | https://openalex.org/A5009645934 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 4 |
| corresponding_institution_ids | https://openalex.org/I2801349226 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/9 |
| sustainable_development_goals[0].score | 0.49000000953674316 |
| sustainable_development_goals[0].display_name | Industry, innovation and infrastructure |
| citation_normalized_percentile.value | 0.46366844 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |