FASTA

Le serveur Fasta de Pasteur:

FASTA (W. Pearson)



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Fasta program

Query sequence File : please enter either :

  1. the name of a file:
  2. or the actual data here:
(sequence format)

Is it a DNA or protein sequence ? DNA protein

Protein Database

Nucleotid Database

Control Options

Optimization Options

Report options

Other Options

Control Options

ktup : sensitivity and speed of the search (protein:2, DNA:6)
OPTCUT : the threshold for optimization. The OPTCUT value is normally calculated based on sequence length
GAPCUT: threshold for joining the initial regions for calculating the initn score
penalty for the first residue in a gap (-12 by default for fasta with proteins, -16 for DNA)
penalty for additional residues in a gap (-2 by default for fasta with proteins, -4 for DNA)
expectation value threshold for displaying scores and alignments

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Optimization Options

band-width used for optimization
unlimited Smith-Waterman alignment for DNA
no limited optimization

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Report options

No histogram
number of similarity scores to be shown
number of alignments to be shown

Alternate display of matches and mismatches in alignments
sequences ranked by the z-score based on the init1 score
both sequences are shown in their entirety in alignments
output line length for sequence alignments (< 200)
start numbering the aligned sequences at position x1 x2 (2 numbers)
display more information about the library sequence in the alignment
write out the sequence identifier, superfamily number, and similarity scores to this file
Do not do statistical significance calculation

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Other Options


filename of an alternative scoring matrix file (BLOSUM50) : please enter either :
  1. the name of a file:
  2. or the actual data here:

(fastx only) penalty for a +1 or -1 frameshift
(tfasta only) only the three forward frames are searched

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Some explanations about the options


Main parameters
Fasta program
fasta/fasta3 - scan a protein or DNA sequence library for similar sequences
tfasta/tfasta3 - compare a protein sequence to a DNA sequence library, translating the DNA sequence library `on-the-fly'.
fastx/fastx3/fasty3 - compare a DNA sequence to a protein sequence database, comparing the translated DNA sequence in three frames, with frameshifts. fasty2 allows frameshifts inside codons.
tfastx3/tfasty3: compare a protein sequence vs a translated DNA db, with frameshifts. tfasty3 allows frameshifts inside codons.
enter either the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application
(but not both)

Optimization Options
band-width used for optimization
Set the band-width used for optimization. -y 16 is the default for protein when ktup=2 and for all DNA alignments. -y 32 is used for protein and ktup=1. For proteins, optimization slows comparison 2-fold and is highly recommended.
unlimited Smith-Waterman alignment for DNA
force Smith-Waterman alignment for output. Smith-Waterman is the default for protein sequences and FASTX, but not for TFASTA or DNA comparisons with FASTA.


Control Options
ktup : sensitivity and speed of the search (protein:2, DNA:6)
ktup sets the sensitivity and speed of the search. If ktup=2, similar regions in the two sequences being compared are found by looking at pairs of aligned residues; if ktup=1, single aligned amino acids are examined. ktup can be set to 2 or 1 for protein sequences, or from 1 to 6 for DNA sequences. The default if ktup is not specified is 2 for proteins and 6 for DNA.
expectation value threshold for displaying scores and alignments
Expectation value limit for displaying scores and alignments. (Typically 10.0 for protein sequence comparisons; 5.0 for FASTX, and 2.0 for DNA sequence comparisons.)

Report options
Alternate display of matches and mismatches in alignments
(MARKX) =0,1,2,3,4. Alternate display of matches and mismatches in alignments.
MARKX=0 uses ':','.',' ', for identities, conservative replacements, and non-conservative replacements, respectively.
MARKX=1 uses ' ','x', and 'X'.
MARKX=2 does not show the second sequence, but uses the second alignment line to display matches with a '.' for identity, or with the mismatched residue for mismatches. MARKX=2 is useful for aligning large numbers of similar sequences.
MARKX=3 writes out a file of library sequences in FASTA format. MARKX=3 should always be used with the 'SHOWALL' (-a) option, but this does not completely ensure that all of the sequences output will be aligned.
MARKX=4 displays a graph of the alignment of the library sequence with repect to the query sequence, so that one can identify the regions of the query sequence that are conserved.
start numbering the aligned sequences at position x1 x2 (2 numbers)
causes fasta/lfasta/plfasta to start numbering the aligned sequences starting with offset1 and offset2, rather than 1 and 1. This is particularly useful for showing alignments of promoter regions.
Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW