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July 30, 2024: NPS@ updated (see NEWS).

A brief introduction to FASTA
FASTA algorithm is an improvement of FASTP algorithm described in 1985. It allows the comparison of one sequence against a database of one or several sequences in order to found similar sequences to the query one. The sequences can be protein or DNA ones. The speed and the sensitivity of the search depend on the word size (ktup) used in the first step of the algorithm.

Availability in NPS@
FASTA is available :

• for query protein sequence
• for query nucleotide sequence
• when you work with a sequence in NPS@
• when you work with a database in NPS@

Parameters
Some parameters are currently not available for the user.
By default the number of description and the number of alignment are set to 500.
The word size (ktup) is set to 2 (less sensitive but faster).
The expected threshold is set to 10.0.
The comparison matrix is BLOSUM50.
The gap opening penalty is -12 and gap extending penalty is -2.
To retrieve these informations see the line "Information and statistics : [FASTA]" in NPS@ FASTA result file.

NPS@ FASTA output example
The NPS@ FASTA output is divided into three parts.

• PART 1:
  In this part, you have :
  • a graphic indicating the similarity found along the query sequence. It's computed with FASTA pairwise sequence alignments
  • a form to select subject sequences, you can select sequences by indicated the maximal E threshold to do it (by default NPS@ sets it to 1e-6), you can also select subject sequences matching a particular region of the query
  
  


• PART 2:
  It's the FASTA description block in a 'HTMLized' form.
  You can see :
  • a checkbox to select/unselect subject sequence
  • the NPSA link allows you to apply NPS@ methods on the corresponding sequence after it is extracted from the query database
  • the database link to retrieve the database entry
  • the alignment link (on expected value) to see FASTA alignment between the query sequence and the current subject sequence
  • the number of displayed sequences
  • the number of selected sequences
  
  


• PART 3:
  You have :
  • an extract form to extract selected sequence and make a database. You can extract full or partial sequences.
    The full extract is made from the database.
    The partial extract, is made for subject sequence that match the query one in the indicated region. The extracted sequence is retrieved from the FASTA alignment. You can set the minimal length of the extracted sequence
  • a checkbox to add your query sequence in the created database
  • a checkbox to remove identical sequences in the created database
  • a link on FASTA information and statistics
  • a link on the original FASTA result text file
  
  

References

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