Note - this is not about Next-gen sequencing or other major deep-sequencing projects
I do a lot of simple (cheap) basic sanger sequencing of plasmids with companies like Macrogen and Genewiz. When I'm sequencing a large insert I often have to use 6-8 primers to get full coverage (at least 2X) of my insert.
Each primer generates approx 700 bp of good clean data.
I then align each 700bp fragment with the reference and then using MS word I arrage all my sequences to see if I have any mismatches that occurred during cloning.
Is there an easier program that will allow me to quickly stitch together my 700bp fragments so that I can simply align the one 'master' seq file with my ref seq? (Usable by someone who isn't very good with RStudio or complex bioinformatics)
Using programs like clustal or ApE to do each one individually works fine but it is tedious, a little slow, and its easy to accidentally copy-paste a sequence wrong.
Thanks!
Using a text editor like WORD for gene or genome assembly is certainly not the best way to go. It sounds like you are not trying to assemble complete plasmid sequences of 100Kb or so, but just an insert of interest that you have inserted into a cloning vector plasmid. Advice on "genome assembly" is probably overkill for that.
https://f1000research.com/articles/7-148
https://genome.cshlp.org/content/27/5/xi.full.html
I have not used the SeqTrace program metioned above, but I looked at it, and it is only available for Windows operating system. You may want to look for others if you using Mac or UNIX machines. At the very least you need a mulitple sequence alignment editor (BioEdit for Windows, AliView ofr Mac)
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
http://ormbunkar.se/aliview/
These have many built-in functions such as reverse-complement the selected sequence(s), and align the whole set or a subregion.
Gene and Genome browsers such as Artemis can be invaluable for studying the assembled region for open reading frames, codon use bias, etc...
https://www.sanger.ac.uk/science/tools/artemis
Using a text editor like WORD for gene or genome assembly is certainly not the best way to go. It sounds like you are not trying to assemble complete plasmid sequences of 100Kb or so, but just an insert of interest that you have inserted into a cloning vector plasmid. Advice on "genome assembly" is probably overkill for that.
https://f1000research.com/articles/7-148
https://genome.cshlp.org/content/27/5/xi.full.html
I have not used the SeqTrace program metioned above, but I looked at it, and it is only available for Windows operating system. You may want to look for others if you using Mac or UNIX machines. At the very least you need a mulitple sequence alignment editor (BioEdit for Windows, AliView ofr Mac)
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
http://ormbunkar.se/aliview/
These have many built-in functions such as reverse-complement the selected sequence(s), and align the whole set or a subregion.
Gene and Genome browsers such as Artemis can be invaluable for studying the assembled region for open reading frames, codon use bias, etc...
https://www.sanger.ac.uk/science/tools/artemis
This might help as well
https://www.researchgate.net/post/How_to_assembly_forward_and_reverse_sequences_in_Sanger_sequencing
If you have not yet found what you were looking for, I think CLC sequence viewer does the job. I did similar work to sequence a gene with several primer pairs. The software is free and good for the task you described.
https://www.qiagenbioinformatics.com/products/clc-sequence-viewer/latest-improvements/current-line/
You can use FastPCR software - Clustering tool:
https://primerdigital.com/fastpcr.html
The CLC workbench platforms (Main Workbench and Genomics Workbench) both do what would want and have a specifically designed set of tools for Sanger/Capillary sequencing data - including an assembler that quickly assembly Sanger reads into a single contig. The CLC Viewer that Ahmed Warsame mentioned is technically no longer available as a separate product - but it’s built into Main Workbench and Genomics Workbench and is active when you use them with a license - there’s really no difference.
theres actually a nice tutorial on the Sanger tools are here : http://resources.qiagenbioinformatics.com/tutorials/Assemble_sequences.pdf
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