bases and low complexity

USAGE SUMMARY

The phrase "bases and low complexity" is correct and usable in written English.
It can be used in contexts discussing foundational elements or components that are simple or not intricate in nature. Example: "In our analysis, we focused on the bases and low complexity of the system to ensure a clear understanding of its functionality."

✓ Grammatically correct

Science

Human-verified examples from authoritative sources

Exact Expressions

5 human-written examples

Cleaning involved masking of poor quality bases and low complexity sequences such as polyA tails.

BMC Genomics

Targets for masking included poly A/T tails, ends rich in undetermined bases, and low complexity sequences.

BMC Genomics

Targets for masking include poly A/T tails, ends rich in Ns (undetermined bases) and low complexity sequences.

BMC Plant Biology

Reads were preprocessed using PRINSEQ-lite 0.20.4 and FastQC 0.10.1 (trimming reads and bases < 25 PHRED, removing exact duplicates, reads with undetermined bases, and low complexity reads using Dust filter = 30) [ 15].

BMC Medical Genomics

First, we processed raw sequence reads to remove the 3' adaptor, "N" bases, and low complexity and sno/t/rRNA (small nuclear/transporter/ribosomal RNA) sequences, and grouped the remaining reads according to the number of unique sequences, resulting in 19,670,792 unique sequences between 20 24 nucleotides (nt) (Table 1).

BMC Genomics

Human-verified similar examples from authoritative sources

Similar Expressions

55 human-written examples

First, the DNA paired-end read library was filtered according to base-call quality (25 of the first 35 bases from the 5′ end must be better than a quality score of 30 for read retention), removing sequence reads which contained ambiguous base-calls, and low complexity (sequences where 85% or more of the bases consist of the same nucleotide).

BMC Genomics

Both insertions mapped to intergenic regions as sequences of a few tens of base pairs and low complexity.

BMC Genomics

Most of the spurious reads were short (average: 40 bases) and low-complexity (i.e. rich in nucleotide repeats).

BMC Genomics

As a quality control, we used BLAST [ 10] to re-map all reads to the Arabidopsis genome [ 11] with a word length of 9 bases and low-complexity filtering turned off.

BMC Plant Biology

After the cross_match finishes, SeqClean removes undetermined bases, poly (A) tails and low complexity regions.

BMC Plant Biology

All physical sequences were trimmed to remove vector, adapter and low complexity regions based on the UniVec (http://www.ncbi.nlm.nih.gov/Univec) and RepBase databases [ 86] using stringent cutoff parameters.

BMC Genomics

Expert writing Tips

Best practice

When discussing DNA sequencing or data processing, use "bases and low complexity" to clearly denote the removal of simple, repetitive sequences, ensuring accuracy in downstream analyses.

Common error

Avoid assuming that "low complexity" implies insignificance. In genomics, filtering out low complexity regions is a crucial step for accurate analysis, not an indication that these regions are unimportant biologically.

Linguistic Context

The phrase "bases and low complexity" functions as a descriptive element within scientific texts, particularly in genomics and bioinformatics. It refers to the fundamental units of DNA or RNA sequences and their level of structural simplicity, as seen in Ludwig's examples.

Expression frequency: Rare

Frequent in

Science

100%

Less common in

News & Media

0%

Formal & Business

0%

Academia

0%

Ludwig's WRAP-UP

The phrase "bases and low complexity" is a technical term predominantly found in scientific literature, specifically within genomics and bioinformatics. As highlighted by Ludwig, it describes the fundamental building blocks of DNA or RNA sequences and their structural simplicity. The phrase serves to communicate the need to filter or mask these regions during data processing to enhance accuracy. The register is formal and scientific, reflecting its use in technical contexts. While examples are relatively rare, their presence in authoritative scientific sources underscores the phrase's importance in the field. The recommendation from Ludwig is to use this term accurately in the context of DNA sequencing or data processing.

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

fundamentals and minimal complexity

Replaces "bases" with "fundamentals" to highlight the essential elements, while maintaining the concept of reduced intricacy.

foundational aspects and uncomplicatedness

Reiterates the fundamental nature and the lack of complexity, using slightly different vocabulary.

core components and reduced intricacy

Highlights the main parts and the decreased level of complexity, suitable for technical contexts.

foundations and simplicity

Emphasizes the fundamental aspects and the uncomplicated nature, shifting from technical terminology to more general terms.

essential structures and simplicity

Replaces "bases" with "essential structures" to stress the necessary framework, keeping the idea of simplicity.

primary constituents and straightforwardness

Highlights the main ingredients and the direct nature, fitting technical or descriptive contexts.

basic elements and simplicity

Focuses on the elementary components and their straightforward nature, using more common language.

initial building blocks and clarity

Stresses the starting points and the lucidity, suggesting a construction or developmental process.

underlying principles and ease

Focuses on the foundational rules and the straightforwardness, moving away from the physical "bases".

root elements and plainness

Emphasizes the origin and the unadorned quality, using less formal wording.

FAQs

How is "bases and low complexity" used in scientific research?

In scientific research, "bases and low complexity" often refers to the process of filtering out or masking regions of DNA or RNA sequences that are repetitive or have simple structures. This is done to improve the accuracy of sequence alignment and downstream analyses.

What does it mean to remove sequences with "low complexity"?

Removing sequences with "low complexity" means eliminating repetitive or simple sequences from a dataset. This helps reduce noise and improve the signal-to-noise ratio in genomic analyses.

Why are "low complexity" sequences removed during sequence analysis?

"Low complexity" sequences are removed because they can cause alignment errors and inflate the apparent similarity between unrelated sequences. Removing these regions ensures more accurate and reliable results in sequence analysis.

What are some techniques used to filter "bases and low complexity" regions?

Techniques like DUST filtering, RepeatMasker, and SeqClean are commonly used to identify and remove "low complexity" regions. These tools use algorithms to detect and mask or remove repetitive sequences from genomic datasets.