KEC: unique sequence search by K-mer exclusion
Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences....
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| Published in: | Bioinformatics (Oxford, England) Vol. 37; no. 19; pp. 3349 - 3350 |
|---|---|
| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
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England
Oxford University Press
11-10-2021
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| Abstract | Abstract
Summary
Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications.
Availability and implementation
KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC.
Supplementary information
Supplementary data are available at Bioinformatics online. |
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| AbstractList | Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications.
KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC.
Supplementary data are available at Bioinformatics online. SUMMARYSearching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. AVAILABILITY AND IMPLEMENTATIONKEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online. |
| Author | Beran, Pavel Čurn, Vladislav Stehlíková, Dagmar Cohen, Stephen P |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33755102$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1038/s41598-018-32295-4 10.1094/PDIS-10-18-1819-RE |
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| Copyright | The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021 The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
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| References | Karim (2023051608261159600_btab196-B1) 2019; 103 Panyukov (2023051608261159600_btab196-B3) 2017; 12 Larrea-Sarmiento (2023051608261159600_btab196-B2) 2018; 8 |
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Summary
Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets.... Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by... SUMMARYSearching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer... |
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| Title | KEC: unique sequence search by K-mer exclusion |
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