CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers.
Genomics
; 113(5): 3174-3184, 2021 09.
Article
in English
| MEDLINE | ID: covidwho-1320193
ABSTRACT
As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http//konulabapps.bilkent.edu.tr3838/CoVrimer/.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Software
/
Sequence Analysis, DNA
/
DNA Primers
/
SARS-CoV-2
Topics:
Variants
Language:
English
Journal:
Genomics
Journal subject:
Genetics
Year:
2021
Document Type:
Article
Affiliation country:
J.ygeno.2021.07.020
Similar
MEDLINE
...
LILACS
LIS