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ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes.

Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H - Nucleic Acids Res. (2007)

Bottom Line: Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq.Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region.As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs.

View Article: PubMed Central - PubMed

Affiliation: State Key Lab for Turbulence and Complex System and Department of Biomedical Engineering, Peking University, Beijing 100871, China.

ABSTRACT
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa.

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Related in: MedlinePlus

Sequence logo and spacer length distribution of representative signals for the genomes (A) E. coli k-12; (B) S. coelicolor; (C) A. fulgidus; and (C) Synechocystis sp. PCC 6803. The positional weight matrix of the signal is visualized by a sequence logo in which the height of a letter on a given position is proportional to its occurring frequency. A letter is bottom-up shown if the occurring frequency is lower than that from the background. The consensus is shown below the logo. The spacer length is defined as the distance (or the number of nucleotides) between the TIS and each of all annotated signals, which are calculated by the positional weight matrix visualized in sequence logo.
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Figure 1: Sequence logo and spacer length distribution of representative signals for the genomes (A) E. coli k-12; (B) S. coelicolor; (C) A. fulgidus; and (C) Synechocystis sp. PCC 6803. The positional weight matrix of the signal is visualized by a sequence logo in which the height of a letter on a given position is proportional to its occurring frequency. A letter is bottom-up shown if the occurring frequency is lower than that from the background. The consensus is shown below the logo. The spacer length is defined as the distance (or the number of nucleotides) between the TIS and each of all annotated signals, which are calculated by the positional weight matrix visualized in sequence logo.

Mentions: The browse page is composed of two sections. The first section shows general information for a genome such as organism name, taxonomic group and genomic GC-content. This section also displays a sequence logo (21) and a histogram of the spacer length for each signal (Figure 1). The second section contains TIS annotation with start site and initiation signal for each gene. It shows the gene coordinate, gene identity (PID and gene name), TIS evidence type (i.e. IPT or CDC or HSC or MED), and the predicted signal. It also provides links to the evidence that supports the proposed TIS to be confirmed: PMID or external database links for IPT TIS, conserved domain search results for CDC-TIS and multiple N-terminal sequence alignments among orthologous genes for HSC TIS.Figure 1.


ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes.

Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H - Nucleic Acids Res. (2007)

Sequence logo and spacer length distribution of representative signals for the genomes (A) E. coli k-12; (B) S. coelicolor; (C) A. fulgidus; and (C) Synechocystis sp. PCC 6803. The positional weight matrix of the signal is visualized by a sequence logo in which the height of a letter on a given position is proportional to its occurring frequency. A letter is bottom-up shown if the occurring frequency is lower than that from the background. The consensus is shown below the logo. The spacer length is defined as the distance (or the number of nucleotides) between the TIS and each of all annotated signals, which are calculated by the positional weight matrix visualized in sequence logo.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238952&req=5

Figure 1: Sequence logo and spacer length distribution of representative signals for the genomes (A) E. coli k-12; (B) S. coelicolor; (C) A. fulgidus; and (C) Synechocystis sp. PCC 6803. The positional weight matrix of the signal is visualized by a sequence logo in which the height of a letter on a given position is proportional to its occurring frequency. A letter is bottom-up shown if the occurring frequency is lower than that from the background. The consensus is shown below the logo. The spacer length is defined as the distance (or the number of nucleotides) between the TIS and each of all annotated signals, which are calculated by the positional weight matrix visualized in sequence logo.
Mentions: The browse page is composed of two sections. The first section shows general information for a genome such as organism name, taxonomic group and genomic GC-content. This section also displays a sequence logo (21) and a histogram of the spacer length for each signal (Figure 1). The second section contains TIS annotation with start site and initiation signal for each gene. It shows the gene coordinate, gene identity (PID and gene name), TIS evidence type (i.e. IPT or CDC or HSC or MED), and the predicted signal. It also provides links to the evidence that supports the proposed TIS to be confirmed: PMID or external database links for IPT TIS, conserved domain search results for CDC-TIS and multiple N-terminal sequence alignments among orthologous genes for HSC TIS.Figure 1.

Bottom Line: Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq.Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region.As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs.

View Article: PubMed Central - PubMed

Affiliation: State Key Lab for Turbulence and Complex System and Department of Biomedical Engineering, Peking University, Beijing 100871, China.

ABSTRACT
Correct annotation of translation initiation site (TIS) is essential for both experiments and bioinformatics studies of prokaryotic translation initiation mechanism as well as understanding of gene regulation and gene structure. Here we describe a comprehensive database ProTISA, which collects TIS confirmed through a variety of available evidences for prokaryotic genomes, including Swiss-Prot experiments record, literature, conserved domain hits and sequence alignment between orthologous genes. Moreover, by combining the predictions from our recently developed TIS post-processor, ProTISA provides a refined annotation for the public database RefSeq. Furthermore, the database annotates the potential regulatory signals associated with translation initiation at the TIS upstream region. As of July 2007, ProTISA includes 440 microbial genomes with more than 390 000 confirmed TISs. The database is available at http://mech.ctb.pku.edu.cn/protisa.

Show MeSH
Related in: MedlinePlus