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local-blast

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Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

When to use

• running >50 queries
• building custom databases with -parse_seqids and -taxid
• downloading prebuilt NCBI databases via update_blastdb.pl
• choosing -task variants (megablast/dc-megablast/blastn/blastn-short)
• tuning soft/hard masking
• scaling threads
• extracting hits with blastdbcmd

When not to use

• using Bio.Blast.Applications

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