Installed Fasta

We have currently installed version 3.4 of the FASTA package.
The reference for this tool is:
Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. US 85:2444-2448 

The official Fasta man page is available at this link.

Help for the Bioinformatica Fasta

Explanations for the form options:

1. DB Type
• You can select 3 types of Databases: protein, nucleic acids or a vector database. Selecting first this option will set the correct values to the other selection boxes.
  
2. Search Title
   
• Here you can select the kind of databases you want to be listed: all of them or a specific subset
  
3. DB name
• Select the database you want to run the search against. Only one choice is possible.
  
4. Program
• Depending on the Db type chosen you will see listed these programs
  
1. fasta3 will compare a protein/DNA sequence against the protein/DNA database of your choice (see option DATABASE).
2. fastx/y3 compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in forward and reverse frames.
3. tfastx/y3 compares a protein to a translated DNA data bank
5. Statistical Estimate
   
6. Matrix
• Use this option to set which comparison matrix should be used when searching the database. The default matrix for a protein blast is blosum62. You may choose from a complete list of matrices which should cover various evolutionary constraints.
  
  
7. Lower E-value
• Use this option to set the expectation value lower limit for score and alignment display. For example, a value of 1e-6 prevents library sequences with E()- values lower than 1e-6 from being displayed.
8. Upper E-value
   
• .Use this option to set the expectation value upper limit for score and alignment display.
9. Open Gap
• Penalty for the first residue in a gap (-12 by default for fasta with proteins, -16 for DNA).
10. Extended Gap
• Penalty for additional residues in a gap (-2 by default for fasta with proteins, -4 for DNA). penalty to control gap scoring.
11. 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.
12. Alignments
• Select the number of alignments you want to see displayed in the ouptut file. F
13. K tuple
• Change this value to limit the word-length the the search should use. A word-length of 2 is sensitive enough for most protein database searches. For DNA searches a ktup of 6 is the default. 
14. Sequence
• You can cut and paste or type a nucleotide or protein sequence into the text window. The only accepted format is a FASTA format. This format contains a one line header followed by lines of sequence data. The first line starts with a " >" symbol and is followed by the name of the sequence. The rest of the line is a description of the sequence (optional). The sequence itself is written in the remaining lines. Blanks lines , spaces are ignored. You can input mor ethan one sequence.
• All sequences must follow the IUB/IUPAC standard codes
• All sequences will be checked before running Fasta, and errors will be pointed. Please correct them before resubmitting  the sequence.

And run Fasta ! 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 Fasta results on the web