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Sequence Homology
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Rapid and sensitive sequence similarity searches powered by parallel computing technology
Organism
Homo sapiens
Mus musculus
Rattus norvegicus
Bos taurus
Sus scrofa
Canis familiaris
Gallus gallus
Danio rerio
Takifugu rubripes
Drosophila melanogaster
Caenorhabditis elegans
Oryza sativa
Arabidopsis thaliana
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Escherichia coli
Bacillus anthracis
Bacillus cereus
Streptococcus pneumoniae
Staphylococcus aureus
Human immunodeficiency virus 1
Select an organism
Gene / Protein
*
Terms separated by comma, eg.
BRCA1
,
LEP
Sequence type
Amino acid query vs any type of database
Nucleotide query (translated) vs any type of database
Nucleotide query vs nucleotide database (direct comparison)
Sequence
*
Database
P: NCBI Non-redundant amino acid sequence database
P: Patent database (peptides) (NCBI)
P: PDB (peptides)
P: RefSeq
P: SWISS-PROT
N: All ESTs (NCBI)
N: Human ESTs (NCBI)
N: Mouse ESTs (NCBI)
N: Other ESTs (NCBI)
N: NCBI Human genomic database
N: NCBI Other genomic database
N: GSS database (NCBI)
N: HTGS database (NCBI)
N: NCBI nucleotide sequence database
N: Patent database (nucleotides) (NCBI)
N: PDB (nucleotides) (NCBI)
N: Refseq Genomic
N: RefSeq RNA
N: STS database (NCBI)
Algorithm
ParAlign
Smith-Waterman
Amino Acid Scoring
BLOSUM45, 14+2k
BLOSUM62, 10+k
BLOSUM62, 10+2k
BLOSUM62, 11+k
LOSUM80, 10+k
PAM30, 9+k
PAM70, 10+k
Nucl. acid scoring
+1/-3, 5+2k
+5/-4, 12+4k
Expect Range
0
0.001
0.01
0.1
-
0
0.001
0.01
0.1
1
10
100
1000
10000
100000
Query Strands
Both
Upper
Lower
Maximum Values
Hits
1
10
100
1000
Alignments
1
10
100
1000
Sub-alignments
1
10
100
1000
Search by organism
Select one or more organisms
Eukaryota
Archaea
Prokaryota
Arabidopsis thaliana
Bacillus cereus
Bos taurus
Caenorhabditis elegans
Chlamydomonas reinhardtii
Danio rerio
Dictyostelium discoideum
Drosophilia melanogaster
Escherichia coli K12
Hepatitis C virus
Homo sapiens
Human cytomegalovirus (HCMV)
Mus musculus
Mycobacterium tuberculosis
Mycoplasma pneumoniae
Neisseria gonorrhoeae
Neisseria meningitidis
Oryza sativa
Plasmodium falciparum
Pneumocystis carinii
Rattus norvegicus
Saccharomyces cerevisiae
Salmo salar
Schizosaccharomyces pombe
Takifugu rubripes
Xenopus laevis
Zea mays
Advanced Options
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