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Sequence (BLAST, PSI-BLAST, FASTA)

Searches protein and nucleic acid sequences using the BLAST or FASTA method. Both methods find similar protein or nucleic acid chains in the PDB. PSI-BLAST is used to find more distantly related sequences.

Sequences can be searched in two ways:

• By PDB ID and Chain ID. Type in a PDB ID in the Structure ID text box and select a Chain ID from the pull-down menu. This is useful to find all sequences that are similar to the sequence from the specified chain.
• By sequence. Paste the sequence in one-letter code format in the Sequence text box. Be sure to remove any other information that might be at the top of the pasted sequence.

Note: sequences must be at least 12 residues long. For shorter sequences try the Sequence Motif Search.

The E value, or Expect value, is a parameter that describes the number of hits one can expect to see just by chance when searching a database of a particular size. For example, an E value of one indicates that a result will contain one sequence with similar score simply by chance. The scoring takes chain length into consideration and therefore shorter sequences can have identical matches with high E value.

The Low Complexity filter masks low complexity regions in a sequence to filter out avoid spurious alignments. Low complexity regions in the sequence are displayed as X in the query sequence.

Sequence Identity Cutoff (%) filter removes the entries of low sequence similarity. The cutoff value is a percentage value between 0 to 100.

BLAST: Sequence searching using NCBI's BLAST (Basic Local Alignment Search Tool) Program , Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215: 403-410 (1990)
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs

PSI-BLAST: Sequence searching to detect distantly related evolutionary relationships using NCBI's PSI-BLAST (Position-Specific Iterated BLAST).

FASTA: Sequence search using the program of Pearson, W.R. and Lipman, D.J. Improved tools for biological sequence comparison. PNAS 85: 2444-2448 (1988)