ArticleNucleic acids research2007
GISMO--gene identification using a support vector machine for ORF classification.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Exploring necroptosis-associated genes: implications for immune responses and therapeutic strategies in diabetic foot ulcers.Archives of medical science : AMS · 2026Article
- Machine learning combining external validation to explore the immunopathogenesis of diabetic foot ulcer and predict therapeutic drugs.PloS one · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Article
- Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov.Environmental microbiology reports · 2024Article
- A novel diabetic foot ulcer diagnostic model: identification and analysis of genes related to glutamine metabolism and immune infiltration.BMC genomics · 2024Article
- Identification and immuno-infiltration analysis of cuproptosis regulators in human spermatogenic dysfunction.Frontiers in genetics · 2023Article
- Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae.BMC genomics · 2014Article
- The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection.Molecular plant pathology · 2013Article
- Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.Genome biology and evolution · 2013Article
- Gene prediction in metagenomic fragments based on the SVM algorithm.BMC bioinformatics · 2013Article
- Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.Journal of bacteriology · 2012Article
- Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.BMC genomics · 2012Article
- Article
- Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris.BMC genomics · 2011Article
- A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.PLoS pathogens · 2010Article
- Article
- Integrated application of uniform design and least-squares support vector machines to transfection optimization.BMC biotechnology · 2009Article
- Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.Environmental microbiology · 2009Article
- Efficient computation of absent words in genomic sequences.BMC bioinformatics · 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present the novel prokaryotic gene finder GISMO, which combines searches for protein family domains with composition-based classification based on a support vector machine. GISMO is highly accurate; exhibiting high sensitivity and specificity in gene identification. We found that it performs well for complete prokaryotic chromosomes, irrespective of their GC content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. Using GISMO, we found several thousand new predictions for the published genomes that are supported by extrinsic evidence, which strongly suggest that these are very likely biologically active genes. The source code for GISMO is freely available under the GPL license.
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.