|
BLAST Program Selection Guide | |
| PubMed | BLAST | Entrez | Entrez/Nucleotide | Entrez/Protein | Structure |
| 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 |