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Before generating the database with DNA-BAR the sequences were run through a PERL script that added a reverse complement for each sequence in order to ensure that query sequences would match the database in either the forward or the reverse orientation.
The ORF portion was defined from each sequence, in order to characterize the CDS from the UTR portions, when possible.
Primers were designed at the 3' side of each sequence in order to reduce the risk of error due to short cDNA synthesis using the Primer 3 module of Geneious (Biomatters Ltd., New Zealand).
The results file was analysed using a bespoke Perl program to create an "architecture string" for each sequence, which lists all the domain names in sequence order.
The input sequence order was jumbled five times, and a topology calculated based on each data order.
Assuming that the number of permutation is N and that there are n genes in a co-expressed set, we randomized the sequence order and rearranged the sequence according to the random order for each permutation.
The sequence order measurement of the Lenstar and the OA-2000 was confirmed by the MedCalc Statistical Software version 13.0, MedCalc Software Inc.., Belgium).
However, sequence order in addition to net charge modulates the mineralization of osteoblast cultures.
We proposed a new model that utilizes sequence-order-independent attributes rather than the web page sequence order.
The HsMM uses the sequence order of web page requests to profile normal web browsing behavior.
Figure 5 shows the cross-correlation coefficients of different 'repeating doublets' with their sequence order.
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