<b dir="MyYpaOBe"></b> Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The . gov means it’s official. Federal government websites often end in . gov or VSports app下载. mil. Before sharing sensitive information, make sure you’re on a federal government site. .

Https

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely V体育官网. .

. 2000 Sep 15;28(18):3442-4.
doi: 10.1093/nar/28.18.3442.

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

B Snel  1 , G Lehmann, P Bork, M A Huynen
Affiliations

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

B Snel et al. Nucleic Acids Res. .

Abstract (V体育官网入口)

The repeated occurrence of genes in each other's neighbourhood on genomes has been shown to indicate a functional association between the proteins they encode. Here we introduce STRING (search tool for recurring instances of neighbouring genes), a tool to retrieve and display the genes a query gene repeatedly occurs with in clusters on the genome. The tool performs iterative searches and visualises the results in their genomic context. By finding the genomically associated genes for a query, it delineates a set of potentially functionally associated genes. The usefulness of STRING is illustrated with an example that suggests a functional context for an RNA methylase with unknown specificity. VSports手机版.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Different parts of the result of an example search performed using STRING that detects a potential new functional interaction. The search was started with a gene from Mycoplasma genitalium that codes for a hypothetical tRNA/rRNA methylating enzyme (MG252) as query. The main graphic of the result (A) shows, after the iterations have converged, that the query (the red genes) occur repeatedly in the same gene cluster with cystenyl transfer RNA synthase (the green genes). The table of co-occurences in clusters (B) shows that this organisation is present in six species, twice in closely related species. It recently has been shown that, at least in some species, the cys-tRNA is modified (15,16). Based on the pattern of conserved gene clusters, we propose that MG252 plays a role in the reported modification of the cys-tRNA. The other retrieved genes co-occurring with each other and with our query gene are less frequently connected to MG252 and cys-tRNA synthase, and are absent from the Mycoplasmas. Although this pattern suggests a less intimate involvement with the proposed interaction, the molecular functions still support some sort of functional link: the gene family in light green is homologous to a ribonuclease, and the family in purple is homologous to sugar nucleotidyl transferase. In this example, the iterations provide us with insight into the conserved genomic organisation of the associated genes. The ribonuclease only repeatedly occurs with the query, while the sugar nucleotidyl transferase has itself a very tight association with an hypothetical protein (the blue genes). When one, in the table of co-occurences, clicks on the number of times our query and the cys-tRNA co-occur in the same cluster in distantly related species, the diagram that only displays these organisations is shown (C). The query gene family is in red, while the cys-tRNA is assigned black. These two colours are reserved to denote the genes that this diagram focuses on. Genes from the same orthologous family have the same colour. The red gene symbols aligned above and below MG252 are its orthologues in the other species. The truncated small white gene-like symbols are genes that are located between the genes retrieved via the conserved gene clusters, but that are themselves not conserved in that position. The gene symbols with two colours are assigned to different gene families because they are the result of fusions. An interruption symbol, such as between yacN and cysS, means that the two displayed stretches of the genome are not in the same gene cluster. The lines between the genes symbolise the stretches of DNA in between the genes, and are linked to the DNA sequence of that stretch, while the gene symbols are linked to their GenBank entries.
Figure 1
Figure 1
Different parts of the result of an example search performed using STRING that detects a potential new functional interaction. The search was started with a gene from Mycoplasma genitalium that codes for a hypothetical tRNA/rRNA methylating enzyme (MG252) as query. The main graphic of the result (A) shows, after the iterations have converged, that the query (the red genes) occur repeatedly in the same gene cluster with cystenyl transfer RNA synthase (the green genes). The table of co-occurences in clusters (B) shows that this organisation is present in six species, twice in closely related species. It recently has been shown that, at least in some species, the cys-tRNA is modified (15,16). Based on the pattern of conserved gene clusters, we propose that MG252 plays a role in the reported modification of the cys-tRNA. The other retrieved genes co-occurring with each other and with our query gene are less frequently connected to MG252 and cys-tRNA synthase, and are absent from the Mycoplasmas. Although this pattern suggests a less intimate involvement with the proposed interaction, the molecular functions still support some sort of functional link: the gene family in light green is homologous to a ribonuclease, and the family in purple is homologous to sugar nucleotidyl transferase. In this example, the iterations provide us with insight into the conserved genomic organisation of the associated genes. The ribonuclease only repeatedly occurs with the query, while the sugar nucleotidyl transferase has itself a very tight association with an hypothetical protein (the blue genes). When one, in the table of co-occurences, clicks on the number of times our query and the cys-tRNA co-occur in the same cluster in distantly related species, the diagram that only displays these organisations is shown (C). The query gene family is in red, while the cys-tRNA is assigned black. These two colours are reserved to denote the genes that this diagram focuses on. Genes from the same orthologous family have the same colour. The red gene symbols aligned above and below MG252 are its orthologues in the other species. The truncated small white gene-like symbols are genes that are located between the genes retrieved via the conserved gene clusters, but that are themselves not conserved in that position. The gene symbols with two colours are assigned to different gene families because they are the result of fusions. An interruption symbol, such as between yacN and cysS, means that the two displayed stretches of the genome are not in the same gene cluster. The lines between the genes symbolise the stretches of DNA in between the genes, and are linked to the DNA sequence of that stretch, while the gene symbols are linked to their GenBank entries.
Figure 1
Figure 1
Different parts of the result of an example search performed using STRING that detects a potential new functional interaction. The search was started with a gene from Mycoplasma genitalium that codes for a hypothetical tRNA/rRNA methylating enzyme (MG252) as query. The main graphic of the result (A) shows, after the iterations have converged, that the query (the red genes) occur repeatedly in the same gene cluster with cystenyl transfer RNA synthase (the green genes). The table of co-occurences in clusters (B) shows that this organisation is present in six species, twice in closely related species. It recently has been shown that, at least in some species, the cys-tRNA is modified (15,16). Based on the pattern of conserved gene clusters, we propose that MG252 plays a role in the reported modification of the cys-tRNA. The other retrieved genes co-occurring with each other and with our query gene are less frequently connected to MG252 and cys-tRNA synthase, and are absent from the Mycoplasmas. Although this pattern suggests a less intimate involvement with the proposed interaction, the molecular functions still support some sort of functional link: the gene family in light green is homologous to a ribonuclease, and the family in purple is homologous to sugar nucleotidyl transferase. In this example, the iterations provide us with insight into the conserved genomic organisation of the associated genes. The ribonuclease only repeatedly occurs with the query, while the sugar nucleotidyl transferase has itself a very tight association with an hypothetical protein (the blue genes). When one, in the table of co-occurences, clicks on the number of times our query and the cys-tRNA co-occur in the same cluster in distantly related species, the diagram that only displays these organisations is shown (C). The query gene family is in red, while the cys-tRNA is assigned black. These two colours are reserved to denote the genes that this diagram focuses on. Genes from the same orthologous family have the same colour. The red gene symbols aligned above and below MG252 are its orthologues in the other species. The truncated small white gene-like symbols are genes that are located between the genes retrieved via the conserved gene clusters, but that are themselves not conserved in that position. The gene symbols with two colours are assigned to different gene families because they are the result of fusions. An interruption symbol, such as between yacN and cysS, means that the two displayed stretches of the genome are not in the same gene cluster. The lines between the genes symbolise the stretches of DNA in between the genes, and are linked to the DNA sequence of that stretch, while the gene symbols are linked to their GenBank entries.
See this image and copyright information in PMC

References (V体育2025版)

    1. Dandekar T., Snel,B., Huynen,M. and Bork,P. (1998) Trends Biochem. Sci., 23, 324–328. - PubMed
    1. Overbeek R., Fonstein,M., D’Souza,M., Pusch,G.D. and Maltsev,N. (1998) In Silico Biol., 1, 0009. - PubMed
    1. Overbeek R., Fonstein,M., D’Souza,M., Pusch,G.D. and Maltsev,N. (1999) Proc. Natl Acad. Sci. USA, 96, 2896–2901. - PMC - PubMed
    1. Marcotte E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Science, 285, 751–753. - PubMed
    1. Enright A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Nature, 402, 86–90. - PubMed

Publication types

Substances (V体育安卓版)