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How to write a code for quickly extracting features through a multisequence data file?

3 years ago in Primer , Python , R Programming By Shahira Sheikh

Primer Python R Programming

Hello everyone,

My task is to develop an excel file that contains sequences and primers along with the features of plasmids. The plasmids are more than 1000 in number.

I have already created a list of raw sequence data and now all I need to do is feature extraction. I decided to use SnapGene for this but now that I have come to the point of extraction, I realise that it is a time consuming process to continuously extract features one by one.

I really believe that there is a way in which a code can be developed (whether in R language or in Python language) which can help in automatically creating this file. So, can anyone please help me with that by telling me if there’s such a function?

If there is an effective way, then what am I supposed to do with the binary program? How can I get the information regarding the feature extraction?

Any help is very much appreciated.

All Answers (4 Answers In All)

By Mehtaab Answered 3 years ago

Hi dear, as per my opinion you can use Geneious Prime instead of SnapGene. I can help you in getting quicker gene analysis and feature extraction.

By Ankur Answered 3 years ago

Hello Shahira, I am attaching two user guides for SnapGene as per your issue. I hope these help you in the long run too. Please go through them once. https://help.snapgene.com/m/user_guide/l/878605-import-from-a-database-to-a-collection https://help.snapgene.com/m/user_guide/l/878667-export-feature-data

By Jamaal Answered 3 years ago

Dear Mehtab, I believe you are not well-acquainted with how SnapGene works. I have used it for most of my research work and it is really great when it comes to quick analysis. SnapGene also provides a few third-part alignment tools as well, four to be exact. With the help of these tools, whether it is DNA sequences or RNA sequences, the researcher can extract three or more than that at one time. Same goes with the extraction of clustal omega, protein sequences, and MAFFT. I am attaching a few more user guides below which are not attached by Ankur above. I hope it will help you in a more descriptive understanding. https://help.snapgene.com/m/user_guide/l/1404591-create-a-multiple-sequence-alignment https://help.snapgene.com/m/user_guide/l/878618-export-files-from-a-collection https://help.snapgene.com/m/user_guide/l/878616-export-primers https://help.snapgene.com/m/user_guide/l/1389970-view-features-in-multiple-sequence-alignments Please go through them.

By Shahira Sheikh Answered 3 years ago

Thank you for your answers @Mehtab, @Ankur, and @Jamaal. I will keep these points in mind and will check out the shared links too.

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