SSS - Sequence Similarity Search service

The HGC SSS service integrates BLAST, FASTA, SSEARCH, EXONERATE and TRANS sequence similarity search programs.

Simple query

1. Select search method

2. Select database to search

3. Select sub category of the database

4. Enter query sequence (in FASTA format - example):

5. Specify type of your query sequence

  • Amino acid
  • Nucleic acid

5.5. Exonerate alignment model options(explanation):

  • affine:local
  • affine:global
  • affine:overlap
  • affine:bestfit
  • est2genome
  • coding2genome (take a long time)
  • genome2genome (take a long time)
  • coding2coding (take a long time)
  • ner
  • protein2dna
  • protein2genome
  • ungapped:trans
  • ungapped

6. Click exec button to search

Advanced options

Receiving results also by e-mail

  • E-mail adddress:

Common options

  • Max number of sequences for which scores will be reported:
  • Max number of sequences for which alignments will be reported:
  • Scoring matrix:
  • Opening gap penalty:
  • Extention gap penalty:

Exonerate options

  • Max number of sequences for which scores will be reported:
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