Fasta

<p>FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.</p>

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The current FASTA package contains programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches. Recent versions of the FASTA package include special translated search algorithms that correctly handle frameshift errors (which six-frame-translated searches do not handle very well) when comparing nucleotide to protein sequence data.

FASTA takes a given nucleotide or amino acid sequence and searches a corresponding sequence database by using local sequence alignment to find matches of similar database sequences.</p>

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Protein sequence to be used in PolyPhen query should be pasted in the Amino acid sequence in FASTA format text area of the input form which, as the name implies, accepts only sequences that follow the FASTA format specification described below. More information about FASTA format can be found here.

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The definition line (defline) is distinguished from the sequence data by a greater-than (>) symbol at the beginning. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (optional). Normally, identifiers are simply protein accession, name or Entrez gi's (e.g., Q5I7T1, AG10B_HUMAN, 129295), but a bar-separated NCBI sequence identifier (e.g., gi|129295) will also be accepted. Any arbitrary user-specified sequence identifier can also be used (e.g., CLONE00073452) but you are advised to use sufficiently long unique words in such case. There should be no space between the ">" and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is:</p>

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>gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)

QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE

KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS

VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP

FLFLIKHNPTNTIVYFGRYWSP

Blank lines are not allowed in the middle of FASTA input.</p>

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Sequences are expected to be represented in the standard IUB/IUPAC amino acid and codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., X for unknown amino acid residue).</p>

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The IUB/IUPAC amino acid codes are:</p>

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A &nbsp;alanine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;P &nbsp;proline

B &nbsp;aspartate/asparagine &nbsp;Q &nbsp;glutamine

C &nbsp;cystine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;R &nbsp;arginine

D &nbsp;aspartate &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;S &nbsp;serine

E &nbsp;glutamate &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;T &nbsp;threonine

F &nbsp;phenylalanine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;U &nbsp;selenocysteine

G &nbsp;glycine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;V &nbsp;valine

H &nbsp;histidine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;W &nbsp;tryptophan

I &nbsp;isoleucine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Y &nbsp;tyrosine

K &nbsp;lysine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Z &nbsp;glutamate/glutamine

L &nbsp;leucine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;X &nbsp;any

M &nbsp;methionine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;* &nbsp;translation stop

N &nbsp;asparagine &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- &nbsp;gap of indeterminate length</p>

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