Use BLAST by pasting in a nucleotide or amino acid sequence in FASTA format, or simply using an accession or GI number.

• nucleotide blast - Search a nucleotide database using a nucleotide query
  • Algorithms: blastn, megablast, discontiguous megablast
• protein blast - Search protein database using a protein query
  • Algorithms: blastp, psi-blast, phi-blast
• blastx - Search protein database using a translated nucleotide query
• tblastn - Search translated nucleotide database using a protein query
• tblastx - Search translated nucleotide database using a translated nucleotide query

(PSI) Position Specific Iterated BLAST - Search databases of sequence profiles to find members of the same protein family. First round runs BLAST and constructs a position-specific score matrix (PSSM) from significant hits while iterations use this PSSM as the query on profile databases. Uncovers more distant protein relationships.

(PHI) Pattern Hit Initiated BLAST - Identify proteins that preserve a specified pattern contained within your query. Query includes a protein sequence and a regular expression defining the pattern of interest

(RPS) Reversed Position Specific BLAST - can quickly compare a sequence to a collection of conserved domains (aka motifs, profiles, HMMs). RPS Blast has an option to perform a translated search of DNA sequences against these conserved domains.

MegaBLAST - Optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". It is approximately 10 times faster than more common sequence similarity programs and therefore can be used to swiftly compare two large sets of sequences against each other. An implementation of MegalBLAST is used to assemble clusters in UniGene.

Upload or paste 2 sequences and BLAST them against each other.