FASTA

   STEP 1 - Select your database

• PROTEIN DATABASES
  • UniProt Knowledgebase
  • UniProtKB/Swiss-Prot
  • UniProtKB/Swiss-Prot isoforms
  • UniProtKB/TrEMBL
  • UniProt Clusters
    • UniProt Clusters 100%
    • UniProt Clusters 90%
    • UniProt Clusters 50%

   STEP 2 - Enter your input sequence

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

or Upload a file:

   STEP 3 - Set your parameters

• 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