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. 2016 Mar 24:53:1.29.1-1.29.15.
doi: 10.1002/0471250953.bi0129s53.

UniProt Tools

Sangya Pundir  1 , Maria J Martin  1 , Claire O'Donovan  1 ; UniProt Consortium  1   2   3   4
Affiliations

UniProt Tools

Sangya Pundir et al. Curr Protoc Bioinformatics. .

Abstract

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the 'BLAST' tool for sequence similarity searching, the 'Align' tool for multiple sequence alignment, and the 'Retrieve/ID Mapping' tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa. This unit provides three basic protocols, three alternate protocols, and two support protocols for using UniProt tools.

Keywords: UniProt; navigation; search; tutorial.

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Figures

Figure 1
Figure 1
Blast link in UniProt header
Figure 2
Figure 2
Blast query input page
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Figure 3
BLAST results page
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Figure 4
UniProtKB search results page
Figure 5
Figure 5
Selecting a protein to BLAST from the results page
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Figure 6
Running BLAST on a protein from the protein entry page
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Figure 7
Running BLAST from the basket
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Figure 8
Align query input page
Figure 9
Figure 9
‘Align’ multiple protein sequences from UniProtKB results page
Figure 10
Figure 10
‘Align’ results page
Figure 11
Figure 11
Aligning proteins from the basket
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Figure 12
Retrieve/ID Mapping query input page
Figure 13
Figure 13
UniProtKB batch results
Figure 14
Figure 14
Mapping UniProtKB IDs to an external database
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Figure 15
BLAST results viewed by ‘Taxonomy’
Figure 16
Figure 16
‘Align’ results page options to highlight annotations and amino acid properties
See this image and copyright information in PMC

References

    1. Huang Hongzhan, McGarvey Peter B, Suzek Baris E, Mazumder Raja, Zhang Jian, Chen Yongxing, Wu Cathy H. A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics. 2011 Apr 15;27(8):1190–1191. 2011. - PMC - PubMed
    1. Ladunga I. Finding Homologs in Amino Acid Sequences Using Network BLAST Searches. Current Protocols in Bioinformatics. 2009;25:3.4, 3.4.1–3.4.34. - PubMed
    1. Simossis V, Kleinjung J, Heringa J. An Overview of Multiple Sequence Alignment. Current Protocols in Bioinformatics. 2003;3:3.7, 3.7.1–3.7.26. - PubMed
    1. UniProt C. UniProt: a hub for protein information. Nucleic acids Res. 2015;43:D204–D212. - PMC - PubMed

Publication types

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