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BLAST (Basic Local Alignment Search Tool) is a sequence similarity search program that finds matches between a tag sequence and human and non human sequences available in databases [ 19].
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Conventional affinity tags are fused as a tag sequence at the DNA level.
If a tag sequence is long enough, the tag matches only one genomic coordinate.
In principle, the oligo tag will ligate to the physical chromosomal termini and the boundary between the tag sequence and the phage genomic sequence will indicate the original physical ends of the phage chromosome.
Therefore, one of the significant advantages of the ECHO probe in tag technology is that the probe does not require either a long tag sequence for fluorescent probe binding or a long spacer sequence to avoid interference between tag-binding probes.
In this technology, longer spacers are necessary between repeated tag sequences to avoid fluorescence quenching by the energy transfer between tag-binding probes.
Correlations between replicate tag sequencing results and between replicate MTP-based microarray results were similar.
To map the DGE tags, the sequenced raw data were filtered to remove low quality tags (tags with an unknown nucleotide "N"), empty tags (no tag sequence between the adaptors) and tags with only one copy number (which might result from sequencing errors).
Specifically comparing between humans and chimpanzees, there is a high correlation of both tag sequence and expression levels in noncoding tags for many partitions (although somewhat less strong than those between tags within exons) (supplementary table 2, Supplementary Material online).
To investigate the variability between tag sequences, each allele-specific extension primer was designed with two alternative tag sequences.
To map the DGE tags, the sequenced raw data were filtered to remove low quality tags (tags with unknown nucleotide "N"), empty tags (no tag sequence between the adaptors) and tags with only one copy number (which might result from sequencing errors).
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