BLIMPS
BLIMPS looks for specific blocks or domains of sequence similarity. A protein may overall have relatively low similarity to another protein, but if it has high similarity in specific important regions it may have the same activity and be a homologous protein. BLIMPS compares a protein or nucleic acid sequence against the BLOCKS database of conserved protein motifs. The scores for high scoring BLOCKS found within the query sequence are totalled and a family classification is made based on the total score for each block found in the query sequence. Individual block scores are listed beneath the family classification along with the highest scoring alignments. Blimps is complimentary to RPSBLAST which evaluates overall similarity rather than specific regions within the program.
If you use this tool, please cite: Henikoff, J G, Greene, E A, Pietrokovski, S, and Henikoff, S. (2000) Increased coverage of protein families with the Blocks Database servers Nucl. Acids Res. 28(1) 228-230.
INPUT = Protein or Nucleic Acid Sequences.
TEST FILES
Input file: blimps_in.txt
Output file: blimps_out.txt