Means it is in the reverse orientation (" it anneals to theĬomplementary strand and points backwards").īoth primers has also some (partial) homology in other parts of Identical to the pGT4 DNA sequence from position 1586 to 1557, which If you would do the same for the longer (30 nucleotides long) Standard Primer has perfect homology (is identical to) with the pGT4 sequence So, in this example, the smaller (17 nucleotides long) Standard GeneTech The resulting output screen shows the position in the pGT4 sequence, where Then, scrol down to click the BLAST button: the smaller of the two Standard GeneTechĪnd a Subject Sequence (e.g. Nucleotide blast program in the Basic BLAST section:Ĭhoose the Align two or more sequences option:Īnd enter a Query Sequence (e.g. Sequences), for example to find out where a primer exactly anneales on a Sequences you can use the BLAST program bl2seq (Blast Two Sequences: For example: use ApE to number the nucleotides in this sequence: Use the Text Map feature and if you would leave this default settings: You would get this: A lignment Recognition site vs the position of the cut made by the restriction This has to do with how the two programs deal with the position of the EMBOSS gives sizes 35 for the Lambda x EcoRI/BamHI end Program, (right click to Save Target As "ApE"ĮMBOSS and ApE calculate fragment lengths differently Į.g. Restriction sites and fragment lenghts in DNA sequences
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