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• Services Help Index
• What Tool should I Use?
• Which Database Can I Search?
• Which Sequence Format Will the System Accept?
• What are Amino Acid and Nucleotide Codes?
• What is a DNA Strand?
• What is a Reading Frame?
• Molecule Types
• How do I Choose an Optimal Alignment?
• What is a Substitution matrix? Which One Should I Use?
• What Are Gap Penalties?, What Value Should I Use?
• References

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• EBI
• Help

Help - Common Parameters used for Tools

• EMAIL
  
  Your email address must consist of a user name followed by the `at´ sign (@), followed by your Internet domain. A typical example: joe@ebi.ac.uk. The delivery of results via email depends upon your email address, so please make sure you type it correctly.

• TITLE
  
  You may give your search a name by typing an informative identifier here.

• RESULTS
  
  This option lets you choose between interactive and non-interactive submissions. Non-interactive submissions require that you provide us with your email address. We will deliver the results to your email.

• SCORES
  
  Setting this option to any number available in the menu allows you to set to maximum number of reported scores in the output file.

• ALIGNMENTS
  
  Setting this options to any number available in the menu allows you to set the maximum number of reported alignments in the output file.

• STRAND
  
  When searching with DNA sequences, this options lets you specify to the programs whether you wish to search with the forward or the reverse strand. More about DNA strands

• EXPECTATION VALUE UPPER LIMIT
  
  Here you may set the expectation value upper limit for score and alignment display. The defaults are 10.0 for FASTA with protein searches, 5.0 for translated DNA/protein comparisons, and 2.0 for DNA/DNA searches.

• EXPECTATION VALUE LOWER LIMIT
  
  Expectation value lower limit for score and alignment display. A value of 1e-6 prevents library sequences with E()- values lower than 1e-6 from being displayed. This allows the use to focus on more distant relationships.

• SEQUENCE INPUT WINDOW
  
  You can cut and paste or type a sequence into the large text window. A free text (raw) sequence is simply a block of characters representing a DNA/RNA or Protein sequence. You may also paste a sequence in GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format. Partially formatted sequences will not be accepted. Copying and pasting directly from word processors may yield unpredictable results as hidden/control characters may be present. Adding a return to the end of the sequence may help certain applications understand the input. Some examples of common sequence formats may be seen here.

 

• UPLOAD
  
  You may upload a file from your computer which contains a valid sequence in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot) using this option. Please note that this option only works with Netscape Browsers or Internet Explorer version 5 or later. Some word processors may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden windows characters. Some examples of common sequence formats may be seen here.