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Based on previous work14, 19, we used single-template homology modeling, in order to allow manual sequence alignment adjustments and direct comparisons of templates.
Although the SRCP is not a replacement for manual sequence characterization, it can provide a rapid, high-quality overview of genome sequence content and facilitate subsequent annotation.
Manual sequence inspection was performed to ensure high quality of full-length cDNA sequences.
When subjected to manual sequence analysis, a large number (thirty-three) of these proteins turned out to contain mucin-like PTS repeats (Table S2).
A manual sequence alignment reveals that the specific percent identity between the interferon lambda family and other helical cytokine families is approximately 5% (to type-II interferon), 12% (to type-I interferons), and 15% (to IL10 family members).
The relative positions of antisense miRNA in the PEG11 nucleotide sequences and corresponding PEG11 protein sequences were deduced by using annotated miRNA identified in the UCSC browser, manual sequence inspection and literature information [31].
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PCR products were gel-purified and subjected to automated sequencing on an ABI3100 sequencer (Applied Biosystems, Foster City, CA), or manual sequencing with a T7 Sequenase version 2.0 sequencing kit (Amersham, Piscataway, NJ) in both directions.
After pouring many manual sequencing gels and working with annoying radioactivity, and after many months of negative results, you would find a mutation.
The product was directly sequenced on 6% polyacrylamide gel using a radioactive manual sequencing kit (Sequenase Kit, Amersham) and exposed to X-ray film (Kodak) to visualize.
Studies on stage- and gender-specific expression profiles with parasites of various developmental stages have been carried out with different methodological approaches, from manual sequencing of expression sequence tag (EST) to full-length cDNA cloning, microarray hybridization, and random sequencing [15], [16], [17], [18], [19], [20], [21].
Hereby MGcV provides a visual heart to the manual sequence-based analysis of gene-function and gene-regulation in bacteria.
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