Installed EMBOSS

We have currently installed version 3.0 of the EMBOSS.
The reference for this tool is:
Rice,P. Longden,I. and Bleasby,A.(2000),EMBOSS: The European Molecular Biology Open Software Suite, Trends in Genetics Volume 16, Issue 6, 276-277
The official Water-Needle man page is available at this link.

Help for the Bioinformatica Water-Needle

Explanations for all the form options:

1. Program: Selection of Needle-Wunsch or Smith-Waterman Algorithm
   
• The Needleman–Wunsch algorithm performs a global alignment on two nucleotide or protein sequences.
• The Smith-Waterman algorithm is an algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences.
  
2. Type: Choose a sequence type
• DNA or Proteins, but you should not mix them in the same input file .
3. Gap Open: Gap opening penalty
   
• The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix.
4. Gap Extend: Gap extension penalty
• The gap extension penalty is added to the gap opening penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap opening penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.
5. Matrix
• This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.

And Run ! The next page will show a small alert window, which will provide you with a JobId. If you know the job will take a long time to execute, you can save this JobId (copy it), click on the exit button, and come back later to view the Water-Needle results on the web