ArticleNucleic acids research2008
Signature, a web server for taxonomic characterization of sequence samples using signature genes.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Explaining microbial phenotypes on a genomic scale: GWAS for microbes.Briefings in functional genomics · 2013Review
- Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.BMC genomics · 2013Article
- Bacterial responses to a simulated colon tumor microenvironment.Molecular & cellular proteomics : MCP · 2012Article
- Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments.Microbial informatics and experimentation · 2012Article
- Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.BMC bioinformatics · 2011Article
- Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.PloS one · 2011Article
- Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen.Journal of bacteriology · 2010Article
- Signature genes as a phylogenomic tool.Molecular biology and evolution · 2008Article
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
Signature genes are genes that are unique to a taxonomic clade and are common within it. They contain a wealth of information about clade-specific processes and hold a strong evolutionary signal that can be used to phylogenetically characterize a set of sequences, such as a metagenomics sample. As signature genes are based on gene content, they provide a means to assess the taxonomic origin of a sequence sample that is complementary to sequence-based analyses. Here, we introduce Signature (http://www.cmbi.ru.nl/signature), a web server that identifies the signature genes in a set of query sequences, and therewith phylogenetically characterizes it. The server produces a list of taxonomic clades that share signature genes with the set of query sequences, along with an insightful image of the tree of life, in which the clades are color coded based on the number of signature genes present. This allows the user to quickly see from which part(s) of the taxonomy the query sequences likely originate.
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.