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. 2023 Mar;3(3):e697.
doi: 10.1002/cpz1.697.

UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping

Rossana Zaru  1 , Sandra Orchard  2 ; UniProt Consortium  1   2   3   4
Affiliations

UniProt Tools: BLAST, Align, Peptide Search, and ID Mapping

Rossana Zaru et al. Curr Protoc. 2023 Mar.

Abstract

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2023). The UniProt website receives about 800,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides four main tools. These are the "BLAST" tool for sequence similarity searching, the "Align" tool for multiple sequence alignment, the "Peptide Search" tool for retrieving proteins containing a short peptide sequence, and the "Retrieve/ID Mapping" tool for using a list of identifiers to retrieve UniProt Knowledgebase (UniProtKB) proteins and to convert database identifiers from UniProt to external databases or vice versa. This article provides four basic protocols and seven alternate protocols for using UniProt tools. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Basic local alignment search tool (BLAST) in UniProt Alternate Protocol 1: BLAST through UniProt text search results pages Alternate Protocol 2: BLAST through UniProt basket Basic Protocol 2: Multiple sequence alignment in UniProt Alternate Protocol 3: Align tool through UniProt results pages and entry pages Alternate Protocol 4: Align tool through UniProt basket Basic Protocol 3: Peptide search in UniProt Basic Protocol 4: Batch retrieval and ID mapping in UniProt Alternate Protocol 5: Retrieve/ID Mapping tool through UniProt text search results pages and BLAST and Align results pages Alternate Protocol 6: Retrieve/ID Mapping tool through UniProt basket Alternate Protocol 7: Retrieve/ID Mapping tool through UniProt search box.

Keywords: BLAST; UniProt; alignment; navigation; search; tutorial.

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Conflict of interest statement

Conflict of Interest

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Tools link in UniProt Web site header.
Figure 2
Figure 2
BLAST query input page.
Figure 3
Figure 3
Tool results dashboard page.
Figure 4
Figure 4
BLAST results page.
Figure 5
Figure 5
UniProtKB search results page.
Figure 6
Figure 6
Selecting a protein to BLAST from the results page.
Figure 7
Figure 7
Running BLAST on a protein from the protein entry page.
Figure 8
Figure 8
Adding protein entries to the basket.
Figure 9
Figure 9
Running BLAST from the basket.
Figure 10
Figure 10
Align query input page.
Figure 11
Figure 11
Align query input page with entries in FASTA format.
Figure 12
Figure 12
Tool results dashboard page.
Figure 13
Figure 13
Align results page.
Figure 14
Figure 14
Align multiple protein sequences from UniProtKB results page.
Figure 15
Figure 15
Aligning proteins from the basket.
Figure 16
Figure 16
Peptide search query input page.
Figure 17
Figure 17
Taxonomy restriction in the peptide search query input page.
Figure 18
Figure 18
Tool results dashboard page.
Figure 19
Figure 19
Peptide search results page.
Figure 20
Figure 20
Retrieve/ID Mapping query input page.
Figure 21
Figure 21
Tool results dashboard page.
Figure 22
Figure 22
UniProtKB ID mapping results page.
Figure 23
Figure 23
Mapping UniProtKB IDs to an external database and ID mapping results page.
Figure 24
Figure 24
Mapping UniProtKB IDs from the results page.
Figure 25
Figure 25
Mapping UniProtKB IDs from the basket.
Figure 26
Figure 26
Mapping UniProtKB IDs from the text search box.
Figure 27
Figure 27
Taxonomy filter in the BLAST results page.
Figure 28
Figure 28
Selecting and viewing the query/hit alignment in the BLAST results page.
Figure 29
Figure 29
Customizing columns of the BLAST results table.
Figure 30
Figure 30
Overview display of the Align results page.
Figure 31
Figure 31
Highlighting sequence features in the alignment.
Figure 32
Figure 32
Tree view of the alignment in the Align results page.
Figure 33
Figure 33
Tools dashboard page.
See this image and copyright information in PMC

References

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