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fasta [2007/12/17 15:35] – heidifasta [2008/07/22 13:31] (current) – external edit 127.0.0.1
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 ====== FASTA ====== ====== FASTA ======
 +**[[http://en.wikipedia.org/wiki/FASTA_format|wikipedia: FASTA format]]**\\
 +[[http://www.ncbi.nlm.nih.gov/blast/fasta.shtml|NCBI's FASTA format description]]\\
 +
 +\\
 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.
 +
  
 ===== 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
 +
 +
 +
 +
 +
 +
  
  
 ===== file format ===== ===== file format =====
   * begins with a single-line description, followed by lines of sequence data   * begins with a single-line description, followed by lines of sequence data
-  * description line: 
-    * ">" symbol in the first column 
-    * word following is the identifier of the sequence (optional) 
-    * rest of the line is the description (optional) 
-    * no space between the ">" and the first letter of the identifier 
   * It is recommended that all lines of text be shorter than 80 characters   * It is recommended that all lines of text be shorter than 80 characters
   * The sequence ends if another line starting with a ">" appears (this indicates the start of another sequence   * The sequence ends if another line starting with a ">" appears (this indicates the start of another sequence
-**simple example:**+**simple examples:**
 <code> <code>
 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
Line 27: Line 34:
 GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
 IENY IENY
 +</code>
 +
 +example of a multiple sequence FASTA file:
 +<code>
 +>SEQUENCE_1
 +MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
 +LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
 +IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
 +MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
 +>SEQUENCE_2
 +SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
 +ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
 </code> </code>
  
 === Header line === === Header line ===
   * begins with ">"   * begins with ">"
-  * gives a name and/or a unique identifier for the sequence +  * word following is the identifier and/or name of the sequence (optional) 
-  * and other informations  +  * rest of the line is the description (optional) 
-  * Many different sequence databases use standardized headers, which helps when automatically extracting information from the header. +  * no space between the ">" and the first letter of the identifier 
-  * header line may contain more than one header separated by a ^A (Control-A) character.+  * header line may contain more than one header separated by a ^A (Control-A) character
  
 +\\
 +  * Sequence identifiers:
 +    * Many different sequence databases use standardized headers, which helps when automatically extracting information from the header
 +    * 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: 
 +
 +| GenBank                          | ''gi|gi-number|gb|accession|locus'' |
 +| EMBL Data Library                | ''gi|gi-number|emb|accession|locus'' |
 +| DDBJ, DNA Database of Japan      | ''gi|gi-number|dbj|accession|locus'' |
 +| NBRF PIR                         | ''pir||entry'' |
 +| Protein Research Foundation      | ''prf||name'' |
 +| SWISS-PROT                       | ''sp|accession|name'' |
 +| Brookhaven Protein Data Bank (1) | ''pdb|entry|chain'' |
 +| Brookhaven Protein Data Bank (2) | ''entry:chain|PDBID|CHAIN|SEQUENCE'' |
 +| Patents                          | ''pat|country|number'' |
 +| GenInfo Backbone Id              | ''bbs|number'' |
 +| General database identifier      | ''gnl|database|identifier'' |
 +| NCBI Reference Sequence          | ''ref|accession|locus'' |
 +| Local Sequence identifier        | ''lcl|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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 |       -           | gap of indeterminate length | |       -           | gap of indeterminate length |
  
 +\\
 The amino acid codes supported are: The amino acid codes supported are:
  
Line 102: Line 144:
  
  
-===== How to cite =====+ 
 + 
 + 
 +===== converter ===== 
 +[[http://iubio.bio.indiana.edu/soft/molbio/readseq/|Readseq]] for converting sequence formats to FASTA \\ 
 +[[http://www.bugaco.com/bioinf/|Nexus to Fasta converter]]\\ 
 +[[http://gp2fasta.ovh.org/|GenBank to Fasta conventer]]
fasta.1197902103.txt.gz · Last modified: 2008/07/22 13:30 (external edit)