ArticlePloS one2023
Portable BLAST-like algorithm library and its implementations for command line, Python, and R.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.Frontiers in immunology · 2025Article
- PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models.Scientific reports · 2024Article
- Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.Frontiers in cellular and infection microbiology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files. However, a portable, modular and embeddable implementation of a BLAST-like algorithm, is still missing from our toolbox. Here we present nsearch, a command line tool and C++11 library which provides BLAST-like functionality that can easily be embedded in any application. As an example of this portability we present Blaster which leverages nsearch to provide native BLAST-like functionality for the R programming language, as well as npysearch which provides similar functionality for Python. These packages permit embedding BLAST-like functionality into larger frameworks such as Shiny or Django applications. Benchmarks show that nsearch, npysearch, and Blaster are comparable in speed and accuracy to other commonly used modern BLAST implementations such as VSEARCH and BLAST+. We envision similar implementations of nsearch for other languages commonly used in data science such as Julia to facilitate sequence similarity comparisons. Nsearch, Blaster and npysearch are free to use under the BSD 3.0 license and available on Github Conda, CRAN (Blaster) and PyPi (npysearch).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.