8-Mer FASTA Search ?

Codex Text for Homology

Input Parameters

The 8 amino acid comparison search is based only on the criteria of exact residue matching to an 8 amino acid length in a COMPARE allergen sequence. Similar to the 80-mer search, an 8-mer search begins with the process of breaking down an input sequence into its composite 8 amino acid length sections. Each section, or 8-mer, is then a query input sequence for separate algorithm and database comparison that reports any exact matches with allergen(s). There is no E-value utilized for examining alignments and FASTA is not involved in this process. A match is referred by Codex Alimentarius (2003 and 2009) as a type of short-length, exact match bioinformatic alignment that may add value to understanding relevant alignments between novel or new proteins and allergen sequences. This type of search has been shown to possess a high degree of false positive outcomes in alignments due to the short length and non-specificity to allergens compared to non-allergens.(Silvanovich et al., 2009)

Input Sequence:

FASTA Algorithm Input Parameters

FASTA Algorithm Output Criteria to Help Interpret Significance

Criteria Based on % Overlap
Criteria Based on E-Value
% Identity Threshold = Alignment Overlap:
E-Value Threshold:

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The submit button ("Execute FASTA Search") is initially disabled (gray button) and will only be enabled (green button) if the input sequence is formatted properly (i.e: first line starting with right angle bracket sign ">"; actual sequence starting in the second line; no invalid characters in the sequence line).

Please note that 80 and 8 mer FASTA search take longer to run. If you do not get a response within three minutes, please reduce the length of your sequence.