Blast

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Description

The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Availability

  • Blast+ version 2.6.0
    • module blast+-2.6.0
  • Blast+ version 2.2.29
    • module blast+-2.2.29
  • Blast+ version 2.2.27
    • module blast+-2.2.27
  • Blast+ version 2.2.26
    • module blast+-2.2.26
  • Blast version 2.2.26
    • module blast-2.2.26

BlastDB

We maintain a local copy of several Blast databases – see the /storage/projects/BlastDB directory. All available databases are described at NCBI web. We mirror all of them. Last update of the offline copy is october 2016. If you need to update DBs or to add some new, please contact the user support meta@cesnet.cz. Databases are ready to use. For your blastn/blastp/tblastx etc. job, use only database base name e.g. nt, nr, wgs, refseq_genomic (-db option).

Use

module add blast-2.2.26   # Blast
module add blast+-2.2.27  # Blast+

then you may run the Blast binaries (see /software/blast-2.2.26/bin, resp. /software/blastPlus-2.2.26/bin or /software/blast-2.2.27/bin).

BLAST programs:

  • blastp - compares an amino acid query sequence against a protein sequence database
  • blastn - compares a nucleotide query sequence against a nucleotide sequence database
  • blastx - compares a nucleotide query sequence translated in all reading frames against a protein sequence database
  • tblastn - compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
  • tblastx - compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database

BLAST command line - manual and examples:

  • https://www.ncbi.nlm.nih.gov/books/NBK279675/
  • blast database: makeblastdb -input_type fasta -in FASTA_FILE -dbtype nucl -title NAME -out NAME
  • blastn: blastn -db DATABASE_NAME -query INPUT_FASTA -out OUTPUT_NAME -max_target_seqs 1 -evalue 1e-5 -num_threads 8
  • blastp: blastp -db DATABASE_NAME -query INPUT_FASTA -out OUTPUT_NAME -max_target_seqs 1 -evalue 1e-5 -num_threads 8
  • tblastx: tblastx -db DATABASE_NAME -query INPUT_FASTA -out OUTPUT_NAME -max_target_seqs 1 -evalue 1e-5 -num_threads 8
  • blastx: blastx -db DATABASE_NAME -query INPUT_FASTA -out OUTPUT_NAME -max_target_seqs 1 -evalue 1e-5 -num_threads 8
  • tblastn: tblastn -db DATABASE_NAME -query INPUT_FASTA -out OUTPUT_NAME -max_target_seqs 1 -evalue 1e-5 -num_threads 8

Documentation

http://www.ncbi.nlm.nih.gov/books/NBK1762/

Licence

It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.

Program manager

meta@cesnet.cz

Homepage

http://blast.ncbi.nlm.nih.gov