BLAST (Basic Local Alignment Search Tool) is the most frequently used sequence homology search tool. Given a probe sequence (nucleotide or protein), BLAST compares it to a sequence database and picks out sequences with significant similarity to the probe sequence. BLAST uses a heuristic search protocol, which makes search very fast compared to non-heuristic methods. The heuristics used may however cause BLAST to fail to find all significant hits.

The command line version of NCBI-BLAST allows a user to modify all parameters of BLAST, to use special methods like PSI-BLAST and PHI-BLAST, and to analyze large data sets.

In Taito you can use pb (Parallel Blast) command for large sets of query sequences. The pb program splits a large search jobs into several subjobs, that can be executed simultaneously (more below).

The most commonly used BLAST commands are:

  • blastn search hits for a nucleotide sequence from nucleotide database
  • blastp search hits for a protein sequence from protein database
  • blastx search hits for a nucleotide sequence from protein database
  • psiblast do iterative search for a protein sequence from protein database
  • rpsblast search hits for a protein sequence from protein profile database
  • rpstblastn search hits for a nucleotide sequence from protein profile database
  • tblastn search hits for a protein sequence from nucleotide database
  • tblastx search hits for a nucleotide sequence from nucleotide database by using the protein translations of both query and database sequences.

Oter blast commands

  • blastdbcmd retrieve a sequence or a set of sequences form BLAST databases
  • makeblastdb create a new BLAST database
  • blast_formatter reformat a BLAST archive formatted BLAST result file.


Version on CSC's Servers

Taito: NCBI BLAST version 2.7.1
FGI grid: NCBI BLAST version 2.6.0
Chipster graphical data analysis interface


At CSC, BLAST searches can be executed in several ways:


To use the latest BLAST in Taito first give set up command :

module load biokit

After that you can start using the BLAST commands listed above. For example following command would search for sequence homologs form UniProt database for a protein sequence.

blastp -query proteinseq.fasta -db uniprot -out result.txt

You can use -help option to see, what command line options are available for a certain BLAST command. For example 

blastp -help

For example, command:  

blastp -query proteinseq.fasta -evalue 0.001 -db uniprot -outfmt 7 -out result.table

Would run the same search as described above, except that the  e-value threshold would be set to 0.001(-evalue 0.001) and the out put is printed out a a table (-outfmt 7).

Usage of pb (Parallel BLAST)  at CSC

If your query sequence set contains less than 20 sequences then Taito-shell is probable the most effective platforms for the search. However, if your query set contains hundreds or thousands of sequences then utilizing the cluster is more  effective. For this kind of massive blast searches you can utilize the pb command in Taito. pb (Parallel BLAST) is designed for situations, where the query file includes large amount of sequences. It splits the query task into several subjobs, that can be run simultaneously using the resources of the server very effectively. For large sets of query sequences, pb can speed up the search up to 50 fold. Two sample pb commands for

module load biokit

pb blastn -db nt -query 100_ests.fasta -out results.out

pb psiblast -db swiss -query protseqs.fasta -num_iterations 3 -out results.out

Using own BLAST databases with pb

The pb program also allows users to do BLAST searches against their own fasta formatted sequence sets. This is done by replacing the -db option with option -dbnuc (for nucleotides) or -dbprot (for proteins). Example:

pb blastn -dbnuc my_seq_set.fasta -query querys.fasta -out results.out

Using genome data from ensembl with pb

pb command can also automatically retrieve a species specific dataset from the Ensembl or Ensembl genomes servers and use the dataset as the search database. This is done by replacing the -db option with option -ensembl_dna (retrieves the genomic DNA),  -ensenmbl_cdna (retrieves the cDNA sequences)  or -ensembl_prot (retrieves the protein sequences). The latin name of a species or taxonomy index number is given as an argument for the ensembl options. You should use underscore (_) in stead of space in the species name.

For example to compare a set of nucleotide sequences against the human genome, you could use a command like:

pb blastn -query dna_fargments.fasta -ensembl_dna homo_sapiens -out  human_hits.txt

To compare the same dna fragments against the protein sequences, predicted from the chicken genome, you could use command:
pb tblastn -query dna_fargments.fasta -ensembl_prot gallus_gallus -out  chicken_hits.txt

You can see the list of species, available at Ensembl and Ensembl genomes databases with command:
ensemblfetch -names

BLAST databases at CSC

Below is a list of BLAST databases maintained at the servers of CSC.

Name Database Source file
nt NCBI non-redundant nucleotide database
refseq NCBI RefSeq RNA database
refseq_con NCBI RefSeq human contigs
nr NCBI non-redundant protein database
pdb PDB protein structure database
swiss Uniprot/Swiss database
trembl Uniprot/TrEMBL database
uniref100 Uniref100 database
uniref90 UniRef90 database
uniref50 UniRef50 database
Ensembl genomes elect one of the species  with pb options: -ensembl_dna, -ensembl_cdna or -ensembl_pep

Users own BLAST databases

CSC offers three ways to do BLAST queries against users own sequence sets

1. BLAST commands in Chipster
Users can do BLAST searches against their own fasta formatted sequence sets with blast commands in Chipster

2. pb BLAST and gb BLAST
In pb blast own databases are used by replacing the -db option with option -dbnuc (for nucleotides) or -dbprot (for proteins). Example:

pb blastn -dbnuc my_seq_set.fasta -query querys.fasta -oout results.out

3. makeblastdb
You can use command makeblastdb to create a BLAST search database form you own asn1 or fasta formatted sequence set. If you use fasta formatted sequence files, please note that makeblastdb command assumes that the comment lines in the fasta file contain ncbi style names for the sequences ( e.g. gnl|db_name|sequece_id).

You can use EMBOSS command seqret to convert a normal fasta file to a ncbi formatted fasta file. For exmaple:

module load emboss

seqret my_seqs.fasta my_seqs_ncbi.fasta -osf ncbi

After this the BLAST database can be created with command:
makeblastdb -in my_seqs_ncbi.fasta -out my_seqs -parse_seqids

After this you can launch a search command. For example:
blastp -query proteinseq.fasta -db my_seqs -out result.txt

Note that if the BLAST database does not locate in the directory where the search command is executed, then the location of the database must be defined with environment variable BLASTDB

export BLASTDB=/path/to/your/blastdatabse

Note that the -dbprot and -dbnuc options of the pb command (described above) do the database building operations automatically.