short alignment

USAGE SUMMARY

The phrase "short alignment" is correct and can be used in written English.
This phrase is typically used in reference to comparing two or more items that are similar in some way. For example, "After a short alignment of the data, it was clear that the patterns of behavior between the two groups were quite different."

✓ Grammatically correct

Science

Wiki

Human-verified examples from authoritative sources

Exact Expressions

28 human-written examples

Because only the SET domain itself can be aligned across all these diverse sequences, a relatively short alignment (231 aa) is available for tree reconstruction; potentially this could lead to spurious phylogenetic associations.

BMC Evolutionary Biology

The short alignment of PA 405 from Muncy to Hughesville contains the most of the highway's history.

Wikipedia

First appearing in 1942, SR 778 was designated along the short alignment that it currently occupies between SR 101 and SR 19.

Wikipedia

We have found that the main reason for this relatively short alignment is that the IL-2 binding sites adopt different conformations when binding the two partners.

Plosone

Uncertainty in the precise location of the splice junction and short alignment can be further resolved in a subsequent evaluation process described below.

Plosone

Due to the relatively short alignment lengths with non-uniform base composition and quality, we did not model the statistical significance of an alignment analytically, but instead chose an empirical metric.

Plosone

Human-verified similar examples from authoritative sources

Similar Expressions

32 human-written examples

These included very short sequences and genes which had short alignments or that aligned with two different genes within the same genomic region, and were considered sequence or alignment artefacts.

BMC Genomics

In the spirit of classifying systematic alignment errors introduced by [48], we refer to this problem as gap dribble, since short alignments are dribbled along the large gap.

Plosone

BWA-SW, for example, tends to miss short alignments with high error rates, as it does not guarantee to find all local hits due to the heuristic acceleration.

Plosone

This makes them fast for short alignments (small L) but slow for large alignments.

Bioinformatics

In addition to the diagonal alignment, several short alignments are present (Additional file 8).

BMC Plant Biology

Expert writing Tips

Best practice

When discussing the impact of a "short alignment", clearly state the specific consequences, such as reduced statistical power or limited phylogenetic signal.

Common error

Avoid assuming that a longer alignment is always better. A "short alignment" with high-quality data and strong homology can be more informative than a longer alignment with poorly aligned or ambiguous regions.

Linguistic Context

The phrase "short alignment" functions as a descriptive term, where "short" modifies the noun "alignment". It indicates that the alignment being referred to is of limited length. Ludwig AI confirms this through its numerous examples, showing the phrase consistently used to describe alignments lacking extensive sequence data.

Expression frequency: Common

Frequent in

Science

80%

Wiki

15%

News & Media

5%

Less common in

Formal & Business

0%

Encyclopedias

0%

Reference

0%

Ludwig's WRAP-UP

In summary, "short alignment" is a commonly used term, particularly within scientific and technical contexts, to describe sequence alignments with limited length. As Ludwig AI's analysis shows, the phrase is grammatically correct and primarily functions to provide descriptive information about the characteristics of an alignment. While such alignments can be useful in specific situations, it's important to be aware of their potential limitations, such as reduced statistical power or phylogenetic resolution. When using the term, writers should clearly state the implications of the "short alignment" and consider alternative approaches if greater accuracy or robustness is required. Remember that while longer alignments aren't automatically superior, focusing on quality and strong homology is critical regardless of length.

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

small alignment

Uses "small" as a direct synonym for "short".

brief alignment

Replaces "short" with "brief", emphasizing conciseness.

limited alignment

Focuses on the restricted scope or extent of the alignment.

abbreviated alignment

Similar to "brief alignment", but with a slightly more formal tone.

reduced alignment

Emphasizes the decreased length of the alignment.

truncated alignment

Implies that the alignment has been cut short or is incomplete.

compact alignment

Highlights the alignment's efficient use of space or length.

condensed alignment

Suggests that the alignment has been compressed or made shorter.

mini alignment

Uses "mini" to denote a very small or short alignment.

narrow alignment

Suggests an alignment that is limited in its range or scope.

FAQs

How is a "short alignment" used in bioinformatics?

In bioinformatics, a "short alignment" typically refers to a sequence alignment with a limited number of base pairs or amino acids. This can occur due to various reasons, such as fragmented sequences, highly divergent regions, or specific algorithm parameters. These alignments are used in phylogenetic analysis, sequence comparison, and database searching, but may have limitations in resolution or statistical power.

What are the limitations of using a "short alignment" in phylogenetic analysis?

Using a "short alignment" in phylogenetic analysis can lead to several limitations, including reduced phylogenetic signal, poorly supported nodes in the resulting phylogenetic tree, and increased susceptibility to long-branch attraction artifacts. Longer alignments generally provide more robust and reliable phylogenetic inferences.

When is it acceptable to use a "short alignment"?

A "short alignment" may be acceptable when dealing with highly conserved regions, when computational resources are limited, or when the goal is to quickly identify homologous sequences. However, it is crucial to acknowledge the potential limitations and interpret the results cautiously.

What are some alternatives to using a "short alignment"?

If possible, consider using longer sequences or combining multiple "short alignments" to create a larger dataset. Alternative alignment methods, such as profile-based alignment or structure-based alignment, may also improve the accuracy of the results. When possible, fill gaps in the alignment using external resources or explore methods such as "sequence homology".