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Quantitatively, reciprocal analyses showed only a slight increase in average overall inconsistency when compared with replicate analyses (1.29 vs. 1.24-fold difference).
We confirmed these IP/co-IP observations by performing reciprocal analyses whereby C subunits were IP and the co-IP association of R subunits was verified (Fig. 1d).
If one link was found between the pine and spruce chromosomes in both reciprocal analyses, we declared this link as homologous.
In contrast, no significant sequence identity was found in reciprocal analyses between the other rodent malaria and P. falciparum PCENs (data not shown).
In addition, reciprocal analyses with anchors at fragment 4 in neonatal heart and at fragment 2 in neonatal brain confirmed the interactions between these sequences with the Kcnq1 promoter region, underscoring the presence of tissue-specific conformations.
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For each, reciprocal BLAST analyses were used to identify and assemble sets of available sequences, and orthology was investigated through phylogenetic analyses.
To identify gene products which originated from a common ancestor we looked for myxobacterial orthologs (BLASTP E-value ≤10−10) using reciprocal Blastp analyses.
Reciprocal BLAST analyses performed on these best candidate gene models using the nr protein data available at NCBI identified most gene models as their corresponding homologs through the conservation of protein domains.
Searches in the expressed sequence tag (EST) databases of Nicotiana species revealed only a partial Serk3 -like sequence from tobacco, while all other ESTs with extended similarity to BAK1/SERK3 did not identify Arabidopsis SERK3 in reciprocal BLAST analyses and are most likely not functional homologs of SERK3 (see methods).
Attempts to detect a physical complex of 5T4 and CXCR4 have been successful in human tumor cells which exhibit higher levels of 5T4 expression and where pulldown and reciprocal western analyses suggest association of some 5T4 and CXCR4 molecules in non-ionic detergent solubilized lysates (Southgate et al unpublished).
We refined these results by performing subsequent reciprocal blastp analyses against the Arabidopsis proteome.
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