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Response: We performed this modification and the updated sequence regarding the beginning of aacA4 gene is already accessible on GenBank database under the same accession number (DQ236170).
Interactions involving domains and/or residues of that protein sequence then require a corresponding update to ensure that the mapping to the updated sequence is correct.
In order to transfer binding site information in the future, we need to translate the position on the original sequence to the updated sequence or make sure that ID mapping adds only identifiers representing the exact same sequence.
The updated sequence was submitted to GenBank [ U79413] The protein sequences of the bovine, human and mouse BPI-like genes were aligned using the SATCHMO (Simultaneous Alignment and Tree Construction using Hidden Markov mOdels) [ 34] with a window size of 13.
Similarly, the updated sequence data that we have collected has allowed us to generate a second set of pRS backbone vectors with a unique AgeI site by excising the LEU2 marker from LEU2 -marked pRS plasmids using Tth111I and AgeI and subsequently recircularizing the backbone (File S1); the presence of an AgeI site flanking the LEU2 marker in pRS305/315/405/415/425 was previously undocumented.
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Of particular interest, the updated sequences demonstrate the presence of an extra-long isoform of Cpeb2 almost double the previously published size (Fig. 2C, 2D, top isoforms).
For the remaining 13 070 GIs, the original sequences need to be compared to the updated sequences in order to transfer binding site annotation.
Pending the completion of the submission process, the updated sequences and annotations can be accessed at http://www.blugen.org/index.php?page=data.
As mentioned above, using the updated sequences for the ADE2 -marked pRS plasmids, we were able to excise the additional undesired pRS reverse primer binding site and generate pRS backbone vectors with a unique BglII site for the insertion of new marker sequences (File S1).
We hope that the new yeast plasmids introduced in this report as well as the updated sequences for existing plasmids will provide a sufficiently complete and cost-effective set of tools for starting research projects that employ budding yeast as a model.
For the proposed technique, the probability of predicting an updated sequence from its correlation with the previous ones is negligible for an attacker.
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