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Blast [ 31] comparisons which do not require strict sequence identity were carried out to analyze for overlaps between the different assemblies.
The mean and median CRR values were fairly consistent between the different assemblies, with the exception of TA_454 that had lower coverage per CCDS and therefore would provide less sequence information per transcript.
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ALC assisted with analyzing the different assemblies.
The REAPR summary scores reveal large differences between the quality of different assemblies, and show that scores are higher in snake than in bird or fish.
Comparison between the sequences in different assemblies helps us understand why the majority of tags in Region II are polymorphic while a few others are non-polymorphic or undetectable.
It is worth to note significant differences exist between different assemblies.
Although we observe strong, assembly-specific correlations between various metrics, many of these are not shared between different assemblies.
Although many of the discrepancies between the different human genome assemblies are caused by fundamental disparities in the compilation of the sequence information [ 4], it is still evident that the human genome harbors probably significantly more than 40,000 genes and that these genes are not easily identified.
Query 9 compares consensus sequences between different assemblies.
These are as follows: 1. NG50 scaffold length: a measure of average scaffold length that is comparable between different assemblies (higher = better).
To allow comparisons between the assemblies of different assembly programs, singletons and contigs shorter than 100 bp were discarded before subsequent analysis.
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