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GO terms were assigned to all 325 differentially expressed genes between the two cultivars, including those having incomplete alignments to a reciprocal sequence.
A reciprocal sequence homology search facilitated the identification of four homologous noncoding DNA regions between the X and Y chromosomes, spanning 6.7% and 10.6% of the X chromosome derived and Y chromosome derived sequences, respectively, investigated.
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In contrast with other approaches (e.g., phylostratigraphy5,6), we use a large and representative taxon sampling and reciprocal sequence comparison7 combined with Markov clustering8 of complete proteomes to identify homology instead of one-way BLAST.
A different evolutionary history characterizes the two families of repeats and their reciprocal sequence organization typical of human chromosomes 4q and 10q.
The reciprocal sequence TGTGT was also periodically distributed, but its phase was shifted.
Reciprocal sequence analysis identified 23-27 % of contigs which displayed no significant match to any transcript in the other genotype.
Reciprocal sequence analysis revealed that c. 87%% of contigs were expressed in both cultivars, while a small proportion were unique to each genotype.
The region spanning residues 66 156 of HsCENP-M displays the highest structural conservation between GTPases and CENP-M and identified reciprocal sequence similarities in iterative HMM searches.
It is evident that the assignment of transcript orthology relationships based exclusively on reciprocal sequence similarity can produce misleading results if structurally different isoforms are inadvertently considered.
Further investigations of the reciprocal sequence CCCCAT showed equivalent distribution to that of ATGGGG, implying that the motif may be functional regardless of its direction.
The XFL-surrounding genes were identified using the Ensembl and JGI utilities and were verified by reciprocal sequence comparisons at the NCBI website using the BLASTP program.
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