fasta
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| ====== FASTA ====== | ====== FASTA ====== | ||
| + | **[[http:// | ||
| + | [[http:// | ||
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| FASTA format is a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. | FASTA format is a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. | ||
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| ===== format information ===== | ===== format information ===== | ||
| * text based | * text based | ||
| + | * no standard file extension for a text file containing FASTA formatted sequences. FASTA format files often have file extensions like .fa, .mpfa, .fna, .fsa, .fas or .fasta | ||
| ===== Data type handled ===== | ===== Data type handled ===== | ||
| * nucleic acid sequences | * nucleic acid sequences | ||
| * peptide sequences | * peptide sequences | ||
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| </ | </ | ||
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| example of a multiple sequence FASTA file: | example of a multiple sequence FASTA file: | ||
| < | < | ||
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| * Many different sequence databases use standardized headers, which helps when automatically extracting information from the header | * Many different sequence databases use standardized headers, which helps when automatically extracting information from the header | ||
| * NCBI defined a standard for the unique identifier | * NCBI defined a standard for the unique identifier | ||
| - | * they do not give a definitive description of the FASTA defline format, an attempt to create such a format: | + | * they do not give a definitive description of the FASTA defline format, an attempt to create such a format: |
| - | GenBank | + | |
| - | EMBL Data Library | + | |
| - | DDBJ, DNA Database of Japan | + | |
| - | NBRF PIR pir||entry | + | |
| - | Protein Research Foundation | + | |
| - | SWISS-PROT | + | |
| - | Brookhaven Protein Data Bank (1) pdb|entry|chain | + | |
| - | Brookhaven Protein Data Bank (2) entry: | + | |
| - | Patents | + | |
| - | GenInfo Backbone Id | + | |
| - | General database identifier | + | |
| - | NCBI Reference Sequence | + | |
| - | Local Sequence identifier | + | |
| - | </ | + | |
| + | | GenBank | ||
| + | | EMBL Data Library | ||
| + | | DDBJ, DNA Database of Japan | '' | ||
| + | | NBRF PIR | '' | ||
| + | | Protein Research Foundation | ||
| + | | SWISS-PROT | ||
| + | | Brookhaven Protein Data Bank (1) | '' | ||
| + | | Brookhaven Protein Data Bank (2) | '' | ||
| + | | Patents | ||
| + | | GenInfo Backbone Id | '' | ||
| + | | General database identifier | ||
| + | | NCBI Reference Sequence | ||
| + | | Local Sequence identifier | ||
| + | //Anm: Die gi-Nummer ist eine Abfolge von Ziffern, die einen Datenbankeintrag des NCBI markiert.// | ||
| + | \\ | ||
| === Sequence representation === | === Sequence representation === | ||
| * After the header line and comments | * After the header line and comments | ||
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| - | ===== How to cite ===== | + | |
| + | ===== converter | ||
| + | [[http:// | ||
| + | [[http:// | ||
| + | [[http:// | ||
fasta.1197902954.txt.gz · Last modified: 2008/07/22 13:30 (external edit)