Dashboard > Nolan Lab > E. coli Blast > blastchart
Which BLAST tool do I use for different searches?
Use the tables to help you decide which BLAST program to use for your searches. Starting from the query sequence on the left and following the appropriate path to the right, you will see the specific BLAST program best suited for your search ...
If your sequence is NUCLEOTIDE
Length Database Purpose BLAST Program  
20 bp or longer Nucleotide Identify the query sequence MEGABLAST
     (accept batch queries)
Standard BLAST
     (blastn)		 Learn More

Learn More
Find sequences similar to query sequence Standard BLAST
      (blastn)		 Learn More
Find similar proteins to translated query in a translated database Translated BLAST
     (tblastx)		 Learn More
Protein Find similar proteins to translated query in a protein database Translated BLAST
     (blastx)		 Learn More
7 - 20 bp
 Nucleotide Find primer binding sites or map short contiguous motifs Search for short, nearly exact matches Learn More


If your sequence is PROTEIN
Length Database Purpose BLAST program  
15 residues or longer Protein Identify the query sequence or find protein sequences similar to query Standard Protein BLAST
     (blastp)		 Learn More
Find members of a protein family or build a custom position-specific score matrix PSI-BLAST Learn More
Find proteins similar to the query around a given pattern PHI-BLAST Learn More
Conserved Domains Find conserved domains in the query CD-search
     (RPS-BLAST)		 Learn More
Conserved Domains Find conserved domains in the query and identify other proteins with similar domain architectures Conserved Domain Architecture Retrieval Tool
     (CDART)		 Learn More
Nucleotide Find similar proteins in a translated nucleotide database Translated BLAST
     (tblastn)		 Learn More
5-15 residues Protein Search for peptide motifs Search for short, nearly exact matches Learn More


Specialized Database Searches
Query Database Purpose BLAST Program  
Nucleotide
or Protein		 None Compare the query and second sequence directly BLAST 2 Sequences Learn more
The NCBI Draft Human Genome Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Human Genome BLAST Learn More
Mouse Genome Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Mouse Genome BLAST Learn More
Rat Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Rat Genome BLAST page Learn More
Fugu
(Pufferfish)		 Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Fugu rubripes Genome BLAST page Learn More
Zebrafish Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Zebrafish Genome BLAST page Learn More
Arabidopsis thaliana Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Arabidopsis thaliana BLAST page Learn More
Oryza sativa(rice) Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Oryza sativa BLAST page Learn More
Anopheles gambiae
(mosquito)		 Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Anopheles gambiae BLAST page Learn More
Other Eukaryotes
Plasmodium, Amoeba, fungi, etc		 Map the query sequence.
Determine the genomic structure.
Identify novel genes.		 Other Eukaryotes BLAST page Learn More
Microbial Genomes Map the query sequence or identify novel genes Microbial Genome BLAST Learn More
Nucleotide
 UniVec Screen for vector contamination
 VecScreen Learn More
Trace Archives Find matches to unassembled, raw sequence data Trace MEGABLAST Search Learn More
   
   © 2006, Iowa State University
   Please send all of your questions or suggestions to the Nolan Lab Technical Support