Start from one protein sequence or protein structure. Uploading or fetching a PDB/mmCIF structure is recommended because the selected chain can be carried forward as the analysis reference and mapped directly onto the structure after alignment and tree construction.
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Fetch a query sequence
Enter an NCBI protein accession or PDB identifier.
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Required for NCBI sequence retrieval and identification of programmatic requests.
Provide one protein sequence or structure file, or fetch a query by NCBI/PDB identifier.
BLAST parameters
Low-complexity filter
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Adjust short queries
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ClusteredNR is submitted to NCBI using the database identifier nr_cluster_seq and is recommended for interactive homolog retrieval. The full nr database can take substantially longer, especially through the programmatic queue.
BLAST search
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Query validatedCheck the accession or protein sequence.
BLAST submittedReceive the NCBI request identifier.
Search homologsWait for the BLASTP search to finish.
Retrieve sequencesDownload complete proteins for the BLAST hits.
Ready for alignmentTransfer the homolog set to MAFFT + FastTree.