REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer
Insertion of silent mutations allowing for restriction site modification aids in the screening of successful mutants during site directed mutagenesis. Introducing a new restriction site requires the analysis of degenerate sequences within mutant primer. As the total number of degenerate codons incre...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-12-01
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| Series: | SoftwareX |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711021001448 |
| _version_ | 1819095347176144896 |
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| author | Madhavi Latha Yadav Bangaru, PhD Ravi Kumar Medabalimi Sobhan Babu, PhD Nidhanapati K. Raghavendra, PhD |
| author_facet | Madhavi Latha Yadav Bangaru, PhD Ravi Kumar Medabalimi Sobhan Babu, PhD Nidhanapati K. Raghavendra, PhD |
| author_sort | Madhavi Latha Yadav Bangaru, PhD |
| collection | DOAJ |
| description | Insertion of silent mutations allowing for restriction site modification aids in the screening of successful mutants during site directed mutagenesis. Introducing a new restriction site requires the analysis of degenerate sequences within mutant primer. As the total number of degenerate codons increases, the analysis becomes increasingly laborious, time-consuming and prone to errors. Towards this, a software named as ‘REMP’ (for REstriction site in Mutant Primer) was developed and described here. From the input sequence, REMP instantaneously generates degenerate sequences having restriction sites that are 6–8 base pairs in length. The output sequences are arranged based on the number of bases changed compared to the input sequence. REMP software can be installed and run as a stand-alone program on different operating systems. Any user of REMP can edit the list of restriction sites to be considered by the software, without a need for writing a computer code or knowing a program language. |
| first_indexed | 2024-12-21T23:41:51Z |
| format | Article |
| id | doaj.art-cd0ed638cc514d7999cb829537c20ff8 |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-12-21T23:41:51Z |
| publishDate | 2021-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-cd0ed638cc514d7999cb829537c20ff82022-12-21T18:46:12ZengElsevierSoftwareX2352-71102021-12-0116100881REMP software to introduce a screening REstriction site in site-directed Mutagenesis PrimerMadhavi Latha Yadav Bangaru, PhD0Ravi Kumar Medabalimi1Sobhan Babu, PhD2Nidhanapati K. Raghavendra, PhD3Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, IndiaDepartment of Computer Science and Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, IndiaDepartment of Computer Science and Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, India; Corresponding authors.Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, India; Corresponding authors.Insertion of silent mutations allowing for restriction site modification aids in the screening of successful mutants during site directed mutagenesis. Introducing a new restriction site requires the analysis of degenerate sequences within mutant primer. As the total number of degenerate codons increases, the analysis becomes increasingly laborious, time-consuming and prone to errors. Towards this, a software named as ‘REMP’ (for REstriction site in Mutant Primer) was developed and described here. From the input sequence, REMP instantaneously generates degenerate sequences having restriction sites that are 6–8 base pairs in length. The output sequences are arranged based on the number of bases changed compared to the input sequence. REMP software can be installed and run as a stand-alone program on different operating systems. Any user of REMP can edit the list of restriction sites to be considered by the software, without a need for writing a computer code or knowing a program language.http://www.sciencedirect.com/science/article/pii/S2352711021001448Site-directed mutagenesisPython 3Silent mutationRestriction siteDNA mutant primer |
| spellingShingle | Madhavi Latha Yadav Bangaru, PhD Ravi Kumar Medabalimi Sobhan Babu, PhD Nidhanapati K. Raghavendra, PhD REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer SoftwareX Site-directed mutagenesis Python 3 Silent mutation Restriction site DNA mutant primer |
| title | REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer |
| title_full | REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer |
| title_fullStr | REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer |
| title_full_unstemmed | REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer |
| title_short | REMP software to introduce a screening REstriction site in site-directed Mutagenesis Primer |
| title_sort | remp software to introduce a screening restriction site in site directed mutagenesis primer |
| topic | Site-directed mutagenesis Python 3 Silent mutation Restriction site DNA mutant primer |
| url | http://www.sciencedirect.com/science/article/pii/S2352711021001448 |
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