FASTA help

A brief introduction to FASTA
FASTA algorithm is an improvment of FASTP alogithm 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 :

So, for example, you can use FASTA to find similar sequences in a database built from an ACNUC query or after a PATTINPROT search.

Parameters
FASTA parameters are not currently 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.

References


User : public@100.24.209.47. Last modification time : Thu Jan 14 19:02:37 2016. Current time : Sun Aug 18 09:41:30 2019