FASTA

• PROTEIN DATABASES
  • UniProt Knowledgebase (The UniProt Knowledgebase includes UniProtKB/Swiss-Prot and UniProtKB/TrEMBL)
  • UniProtKB/Swiss-Prot (The manually annotated section of UniProtKB)
  • UniProtKB/Swiss-Prot isoforms (The manually annotated isoforms of UniProtKB/Swiss-Prot)
  • UniProtKB/TrEMBL (The automatically annotated section of UniProtKB)
  • UniProtKB Taxonomic Subsets
    • UniProtKB Archaea
    • UniProtKB Arthropoda
    • UniProtKB Bacteria
    • UniProtKB Complete Microbial Proteomes
    • UniProtKB Eukaryota
    • UniProtKB Fungi
    • UniProtKB Human
    • UniProtKB Mammals
    • UniProtKB Nematoda
    • UniProtKB PDB
    • UniProtKB Rodents
    • UniProtKB Vertebrates
    • UniProtKB Viridiplantae
    • UniProtKB Viruses
  • UniProt Clusters
    • UniProt Clusters 100% (UniRef100)
    • UniProt Clusters 100% (SEG filtered version of UniRef100)
    • UniProt Clusters 90% (UniRef90)
    • UniProt Clusters 50% (UniRef50)
  • Patents
    • EPO Patent Protein Sequences
    • JPO Patent Protein Sequences
    • KIPO Patent Protein Sequences
    • USPTO Patent Protein Sequences
    • NR Patent Proteins Level-1
    • NR Patent Proteins Level-2
  • Structures
    • Protein Structure Sequences (PDBe protein structure sequences)
    • Structural Genomics Targets (PSI protein structure sequences)
  • Other Protein Databases
    • UniProt Archive (Sequences from the UniProt Archive UniParc)
    • IntAct (Sequences from IntAct interactors)
    • IDP-IMGT/HLA (Immuno Polymorphism Database-International Immunogenetics project/Human Leucocyte Antigen)
    • IPD-KIR (Immuno Polymorphism Database-Killer-cell Immunoglobulin-like Receptors)
    • IPD-MHC (Immuno Polymorphism Database-Major Histocompatibility Complex)
    • MACiE Annot Pub
    • MEROPS-MPRO (Sequences from the MEROPS scan dataset)
    • MEROPS-MPEP (Sequences from the peptidase or inhibitor domain sequence only)
    • MEROPS-MP (Sequences from the full MEROPS collection)

Enter or paste a PROTEIN DNA RNA sequence in any supported format:

or Upload a file: See example inputs

• PROGRAM
  FASTA FASTX FASTY SSEARCH GGSEARCH GLSEARCH

• MATRIX
  BLOSUM50 BLASTP62 BLOSUM80 PAM250 PAM120 MDM40 MDM20 MDM10 VTML160 VTML120 VTML80 VTML40 VTML20 VTML10
• MATCH/MISMATCH SCORES
  N/A
• GAP OPEN
  default 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 -11 -12 -13 -14 -15 -16 -17 -18 -19 -20 -21 -22 -23 -24 -25 -30 -32 -35 -40 -50 -64
• GAP EXTEND
  default 0 -1 -2 -3 -4 -5 -6 -7 -8 -16
• KTUP
  2 1 N/A
• EXPECTATION UPPER VALUE
  1e-600 1e-300 1e-100 1e-50 1e-10 1e-5 0.001 0.1 1 2 5 10 20 50
• EXPECTATION LOWER VALUE
  0 (default) 1e-300 1e-100 1e-50 1e-10 1e-5 0.001 0.1 1 2 5 10 20 50
• DNA STRAND
  N/A both top bottom
• HISTOGRAM
  no yes
• FILTER
  none seg xnu seg+xnu
• STATISTICAL ESTIMATES
  Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.
• SCORES
  10 20 30 40 50 60 70 80 90 100 150 200 250 500 750 1000
• ALIGNMENTS
  10 20 30 40 50 60 70 80 90 100 150 200 250 500 750 1000
• SEQUENCE RANGE
• DATABASE RANGE
• MULTI HSPs
  no yes
• SCORE FORMAT
  Default -m 8 -- blast tabular -m 8C -- BLAST tabular with comments -m 8Cc -- BLAST tabular with -m 9c alignment encoding and domain information -m 8CC -- BLAST tabular with CIGAR and domain information -m 8CD -- BLAST tabular with variation and domain information -m 9 -- with coordinates scores and %identity -m 9C -- with CIGAR alignment -m 9c -- with encoded alignment -m 9i -- with identity and length
• TRANSLATION TABLE
  N/A Standard Vertebrate Mitochondrial Yeast Mitochondrial Mold Mitochondrial Protozoan Mitochondrial Coelenterate Invertebrate Mitochondrial Ciliate Nuclear Dasycladacean Nuclear Hexamita Nuclear Echinoderm Mitochondrial Flatworm Mitochondrial Euplotid Nuclear Bacterial and Plant Plastid Alternative Yeast Nuclear Ascidian Mitochondrial Alternative Flatworm Mitochondrial Blepharisma Macronuclear Chlorophycean Mitochondrial Trematode Mitochondrial Scenedesmus obliquus Mitochondrial Thraustochytrium Mitochondrial
• ANNOTATION FEATURES
  no yes