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First, we re-mapped the microarray probe sequences into the updated rice genome assembly (Build 5.0 pseudomolecules) to make a valid comparison of the microarray data and the mRNA-Seq data.
For reporting genes by name, IMAGE Clone IDs corresponding to the microarray probe sequences were used to extract UniGene Cluster IDs and names (Build 199 Homo sapiens; Jan 16 2007 [104].
All the probe sequences contained their corresponding microarray probe sequences.
Microarray probe sequences were then chosen based on the combined transcriptome assembly.
Microarray probe sequences were mapped to the hg15 and hg18 UCSC genome builds.
Sequence comparisons were used to map microarray probe sequences to predicted Ensembl transcripts (Ensembl version 19) [ 29].
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The previous microarray probe sequence analysis proved that the microarray probe was a part of intron 4 and either 3' or 5' UTR of novel isoforms.
A forward primer (F6) was designed on the AryANE_v1_00084532 microarray probe sequence.
Annotated Vitis databases, such as EST and microarray probe sequence sets, have been added to the BLAST database (Vitis full sequence BLAST db and Vitis full array BLAST db) that will help the grape scientific community to quickly and efficiently identify and annotate ESTs.
Primer sequences (Table 3) were designed using Primer3 v0.4.0 software [ 65], based on the consensus sequences of microarray probe contig sequences and putative mRNA/EST sequences in Genbank [ 66] and Unigene [ 64].
To create a unigene-based matched tomato-potato microarray probe sets, sequences of 7,637 tomato SGN unigenes (represented by 9,140 tomato microarray printed clones) served as queries to blast against 10,860 potato TIGR unigenes (represented by 15,264 potato microarray printed clones).
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