Protein sequence analysis is essential for studying and predicting protein function and structure, but often protein sequence analysis tools lack the visualization component necessary for interpretation, or they require additional tools for downstream analysis. Looking at the trace file will give you more information than simply looking at the bases provided by your sequencing provider.Use Protean 3D for comprehensive protein sequence analysis in one easy-to-use application! For instance, in the trace file below, you can see that just after base 70 there are multiple peaks in the same location.
Look at the peaks in the area and make sure they are justifiable peaks. Open the trace file and use the search feature in the program to locate the incorrect sequence. ab1 files, such as 4Peaks (Mac), SnapGene Viewer (Mac/PC), FinchTV (Mac/PC), Sequence Scanner (PC), and Chromas (PC).
#ONLINE SEQUENCE ANALYSIS FREE#
There are many free programs available that can open. What program can I use to view my trace file? If the mutation is not an artifact, please email with the sequence, trace file, and primer used. My sequence doesn’t match Addgene’s sequencing result, what should I do?Ĭheck your trace file first the apparent mismatch/mutation may be the result of a mis-called peak in the trace file. The corresponding primer sequence used for each reaction.The original trace file (.ab1 file) provided by your sequencing company or core facility.If you obtain a different sequence than expected and wish to contact Addgene about the accuracy of your plasmid, please email and include: This is an example of a trace file from a high-quality portion of a sequencing reaction:
#ONLINE SEQUENCE ANALYSIS SERIES#
You should receive your sequencing results as a trace file (.ab1) which graphically depicts the sequence as a series of colored peaks corresponding to one of the four nucleotide bases. If you require additional sequencing and need to design a custom primer, Addgene recommends using Addgene's sequencing results as a reference for primer design.Ī good sequencing reaction will produce between 300-900 base pairs of useable sequence. Is your custom primer found within the Addgene sequencing results?
What primers were used by Addgene during quality control?Īddgene lists the primers used to obtain each result above the posted sequence in the "View Sequence" link. Many sequencing cores have a list of common primers that can be requested for no additional charge. There are many widely used, common primers that are often found within the plasmid backbone (See Addgene's Sequencing Primers for reference). The primer should be a minimum of 50 nucleotides and a maximum of 300 nucleotides from your target.Īre there commercially available primers that can be used for sequencing? Is the primer an appropriate distance from the target? Make sure the primer only anneals once within the entire construct. There are a number of factors to consider when selecting sequencing primers, including:
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