bioFOX Sidebar

bioFOX sidebar has the following sections: Nucleotide, Protein, BLAST, Structure, Subcellular localization and Miscellaneous Tools.
Each sections has the following analysis tools.

Nucleotide:

  • Translate Frame (1|2|3|-1|-2|-3)
  • Reverse sequence(s)
  • Complement sequence(s)
  • Reverse Complement sequence(s)
  • Codon Usage

Protein:

  • Send to Prosite: Send protein sequence(s) to Prosite
  • Send to Pfam (sequence(s)): Send protein sequence(s) to Pfam
  • Send to Pfam (Keyword): Send to keyword to Pfam (Keyword alone)
  • Sequence Statistics: Get sequence(s) statistics
  • Send to String DB (Protein): Send sequence(s) to String database (protein submission)
  • Send to String DB (COGs): Send sequence(s) to String database (COG submission)
  • Send to sMART (Normal): Send sequence(s) to SMART database (Normal Mode)
  • Hydropathy Plot: Send sequence(s) for hydropathy plot with a window size of 9
  • Alignment: Send sequences for to EBI's Clustalw server

BLAST/BLAT related:

  • blastn: Send nucleotide sequence(s) to blastn
  • blastp: Send protein sequence(s) to blastp
  • tblastn: Send nucleotide sequence(s) to tblastn
  • PSI-BLAST: Send protein sequence(s) to PSI-BLAST
  • BLAT: Opens a new tab with BLAT url

Structure related:

  • SWISS-MODEL: Send protein sequence(s) to SWISS-MODEL server (Requires email address)
  • 3D-PSSM: Send protein sequence(s) to 3D-PSSM server (Requires email address)

Subcellular localization:

  • Plant: Send protein sequence to Predotar, iPsort, pSORT (Plant networks)
  • Non-Plant: Send protein sequence to Predotar, iPSort, pSORT (Non-plant networks)

Miscellaneous Tools:

  • Filter sequence: Opens a new window with filtered sequence(s)
  • Sequence Search: Opens a new window with numbered residues/nucleotides
  • Pi/Mol. Weight: Opens a new tab with molecular weight

Search Pubmed/Scirus:

  • Pubmed: Right click and select a search term and submit it to Pubmed
  • Scirus: Right click and select a search term and submit it to Scirus
           

Workspace:

  • The workspace feature is to analyze sequences which are available on your computer. Input sequences into the textarea of the workspace page and click submit. You can then select the sequence(s) and analyze them.