Exact(1)
The RT-qPCR data were processed with the sequence detection software version 1.3.1 following the method of Schefe et al. [30].
Similar(59)
Sequences were processed with the Sequencing analysis v 3.7 software (Applied Biosystems) then assembled and manually inspected with a STADEN package ver 1.5.3.
Results on real data processed with the same sequence were less encouraging.
It was a logical choice to compare our samples to the human gut microbiota, because this reference data set has been processed with the same sequencing and bioinformatic technologies developed during the European MetaHIT project (http://www.metahit.eu), which has given rise to several publications on the human metagenome [ 3, 4].
Following amplification, the data was processed with the analysis program Sequence Detection Systems v2.2.2 (Applied Biosystems).
The BLAST program from the National Center for Biotechnology Information (NCBI) (http://www.ncbi.lm.nih.gov/BLAST), processed with the non-redundant sequences (nr) GenBank and the nucleotide database generated from Paracoccidioides spp. structural genome (http://www.broad.mit.edu/annotation/genome/paracoccidioides_brasiliensis/MultiHome.html), was used for the annotation.
The resulting reads were processed with the Illumina BaseCaller during the sequencing step.
The resulting reads (read length 101 bp) were processed with the Illumina BaseCaller during the sequencing step.
Then, the reports were parsed and the sequences processed with the aid of Perl scripts in which different modules from the Bioperl toolkit [ 69] were used.
Raw sequences obtained from the sequencing center were processed with the MOTHUR software [ 49].
Of the 19,937 sequences processed with the current version of FunnyBase, 17,893 (90%) passed one of these quality parameters.
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