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MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle.

Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y - Nucleic Acids Res. (2014)

Bottom Line: In total, 87,983 unique proteins with corresponding localization information were integrated into the database.The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown.The orthologous relations between predicted and experimental localizations were also present.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

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The search options of MiCroKiTS database. (A) The database can be directly queried with one or multiple keywords. (B) The ‘Advanced search’ option allows users to submit a combination of two terms for searching. (C) The database could be searched to retrieve a list of proteins through submitting a list of keywords such as UniProt accessions. (D) The database can be queried with a protein sequence in FASTA format to find identical or homologous proteins. (E) The protein list derived from the search options. (F) The details of the MiCroKiTS protein Aurora kinase B in H. sapiens, while the fluorescence microscope figure for the localizations can also be visualized.
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Figure 2: The search options of MiCroKiTS database. (A) The database can be directly queried with one or multiple keywords. (B) The ‘Advanced search’ option allows users to submit a combination of two terms for searching. (C) The database could be searched to retrieve a list of proteins through submitting a list of keywords such as UniProt accessions. (D) The database can be queried with a protein sequence in FASTA format to find identical or homologous proteins. (E) The protein list derived from the search options. (F) The details of the MiCroKiTS protein Aurora kinase B in H. sapiens, while the fluorescence microscope figure for the localizations can also be visualized.

Mentions: To provide convenient usage, the MiCroKiTS 4.0 database web interface was designed in a user-friendly manner for search and browse. The website contains four search options including one/multiple keywords-based simple search (Figure 2A), ‘Advanced search’ based on a combination of multiple keywords (Figure 2B), multiple keywords based ‘Batch search’ (Figure 2C) and protein sequence-based ‘BLAST search’ (Figure 2D). For example, if a keyword ‘aurora’ in ‘Any Field’ was submitted for a simple search (Figure 2A), the website will return a list of MiCroKiTS proteins, such as Aurora kinase B from H. sapiens in a tabular format with accession, species, and protein/gene names/aliases (Figure 2E). By clicking the accession ‘Q96GD4’, user could visit the webpage of human Aurora kinase with detailed annotation including localizations, PubMed IDs of source references and the orthologs (Figure 2F). For human MiCroKiTS proteins, the representing fluorescent microscope figures were provided by clicking the ‘Show Figures’ (Figure 2F). Furthermore, two terms specified in two areas and combined with operators of ‘and’, ‘or’ and ‘exclude’ could be employed to perform a complex query in ‘Advanced Search’ (Figure 2B). For example, querying the database with ‘human’ in ‘Species’ and ‘aurora’ in ‘Gene/Protein Name’ will return three human aurora kinases (Figure 2B). Alternatively, user could submit a list of keywords to perform a batch search. For example, three human aurora kinases could be retrieved by submitting the list of their UniProt accessions (Figure 2C). Furthermore, user could submit a protein sequence in FASTA format in ‘BLAST Search’ to find homologous MiCroKiTS proteins (Figure 2D). For example, the sequence of human Aurora kinase B could be input in the FASTA format to search homologous proteins in the database. The ‘Advanced Search’, ‘Batch search’ and ‘BLAST Search’ will return the list of searching hits in a tabular format as the simple search (Figure 2E). In addition, there is a checkbox of ‘ONLY experimentally identified MiCroKiTS proteins’ for each search option (Figure 2). If the checkbox is selected, only experimentally identified MiCroKiTS proteins will be queried.


MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle.

Huang Z, Ma L, Wang Y, Pan Z, Ren J, Liu Z, Xue Y - Nucleic Acids Res. (2014)

The search options of MiCroKiTS database. (A) The database can be directly queried with one or multiple keywords. (B) The ‘Advanced search’ option allows users to submit a combination of two terms for searching. (C) The database could be searched to retrieve a list of proteins through submitting a list of keywords such as UniProt accessions. (D) The database can be queried with a protein sequence in FASTA format to find identical or homologous proteins. (E) The protein list derived from the search options. (F) The details of the MiCroKiTS protein Aurora kinase B in H. sapiens, while the fluorescence microscope figure for the localizations can also be visualized.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 2: The search options of MiCroKiTS database. (A) The database can be directly queried with one or multiple keywords. (B) The ‘Advanced search’ option allows users to submit a combination of two terms for searching. (C) The database could be searched to retrieve a list of proteins through submitting a list of keywords such as UniProt accessions. (D) The database can be queried with a protein sequence in FASTA format to find identical or homologous proteins. (E) The protein list derived from the search options. (F) The details of the MiCroKiTS protein Aurora kinase B in H. sapiens, while the fluorescence microscope figure for the localizations can also be visualized.
Mentions: To provide convenient usage, the MiCroKiTS 4.0 database web interface was designed in a user-friendly manner for search and browse. The website contains four search options including one/multiple keywords-based simple search (Figure 2A), ‘Advanced search’ based on a combination of multiple keywords (Figure 2B), multiple keywords based ‘Batch search’ (Figure 2C) and protein sequence-based ‘BLAST search’ (Figure 2D). For example, if a keyword ‘aurora’ in ‘Any Field’ was submitted for a simple search (Figure 2A), the website will return a list of MiCroKiTS proteins, such as Aurora kinase B from H. sapiens in a tabular format with accession, species, and protein/gene names/aliases (Figure 2E). By clicking the accession ‘Q96GD4’, user could visit the webpage of human Aurora kinase with detailed annotation including localizations, PubMed IDs of source references and the orthologs (Figure 2F). For human MiCroKiTS proteins, the representing fluorescent microscope figures were provided by clicking the ‘Show Figures’ (Figure 2F). Furthermore, two terms specified in two areas and combined with operators of ‘and’, ‘or’ and ‘exclude’ could be employed to perform a complex query in ‘Advanced Search’ (Figure 2B). For example, querying the database with ‘human’ in ‘Species’ and ‘aurora’ in ‘Gene/Protein Name’ will return three human aurora kinases (Figure 2B). Alternatively, user could submit a list of keywords to perform a batch search. For example, three human aurora kinases could be retrieved by submitting the list of their UniProt accessions (Figure 2C). Furthermore, user could submit a protein sequence in FASTA format in ‘BLAST Search’ to find homologous MiCroKiTS proteins (Figure 2D). For example, the sequence of human Aurora kinase B could be input in the FASTA format to search homologous proteins in the database. The ‘Advanced Search’, ‘Batch search’ and ‘BLAST Search’ will return the list of searching hits in a tabular format as the simple search (Figure 2E). In addition, there is a checkbox of ‘ONLY experimentally identified MiCroKiTS proteins’ for each search option (Figure 2). If the checkbox is selected, only experimentally identified MiCroKiTS proteins will be queried.

Bottom Line: In total, 87,983 unique proteins with corresponding localization information were integrated into the database.The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown.The orthologous relations between predicted and experimental localizations were also present.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

Show MeSH