Fasta格式的详细说明

http://liucheng.name/770/

>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK

        A --> adenosine           M --> A C (amino)
        C --> cytidine            S --> G C (strong)
        G --> guanine             W --> A T (weak)
        T --> thymidine           B --> G T C
        U --> uridine             D --> G A T
        R --> G A (purine)        H --> A C T
        Y --> T C (pyrimidine)    V --> G C A
        K --> G T (keto)          N --> A G C T (any)
                                  -  gap of indeterminate length

    A  alanine                         P  proline
    B  aspartate or asparagine         Q  glutamine
    C  cystine                         R  arginine
    D  aspartate                       S  serine
    E  glutamate                       T  threonine
    F  phenylalanine                   U  selenocysteine
    G  glycine                         V  valine
    H  histidine                       W  tryptophan
    I  isoleucine                      Y  tyrosine
    K  lysine                          Z  glutamate or glutamine
    L  leucine                         X  any
    M  methionine                      *  translation stop
    N  asparagine                      -  gap of indeterminate length

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Fastq格式的详细说明

Posted on 22 七月 2009 by Lc. ，阅读 197

看清楚，这里所说的是Fastq格式，不是Fasta格式，要了解Fasta格式，请看Fasta格式的详细说明。Fastq格式也是序列格式中常见的一种。下面简单介绍一下FASTQ格式，

A FASTQ file normally uses four lines per sequence. Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). Line 2 is the raw sequence letters. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

FASTQ格式的序列一般都包含有四行，第一行由'@'开始，后面跟着序列的描述信息，这点跟FASTA格式是一样的。第二行是序列。第三行由'+'开始，后面也可以跟着序列的描述信息。第四行是第二行序列的质量评价（quality values，注：应该是测序的质量评价），字符数跟第二行的序列是相等的。

FASTQ格式例子：

@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

例如在NCBI看到的FASTQ格式如下：

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC

至于序列的quality values值，是通过一些算法得出来的。具体也搞不明白，不多讲。另外FASTQ格式是不至一种的，不同的来源会有些差异，如Illumina 1.0 FASTQ 、 Sanger FASTQ等。都是比较特殊的情况。

FASTQ格式与Fasta格式、GenBank等格式的相互转换，看BioPerl指南 – 序列格式的转换

转自柳城博客：http://liucheng.name/825/

FASTQ format

From Wikipedia, the free encyclopedia

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are encoded with a single ASCII character for brevity. It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high throughput sequencing instruments such as the Illumina Genome Analyzer.

[edit] Format

A FASTQ file normally uses four lines per sequence. Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). Line 2 is the raw sequence letters. Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.

A minimal FASTQ file might look like this:

@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

The original Sanger FASTQ files also allowed the sequence and quality strings to be wrapped (split over multiple lines), but this is generally discouraged as it can make parsing complicated due to the unfortunate choice of "@" and "+" as markers (these characters can also occur in the quality string).

[edit] Illumina sequence identifiers

Sequences from the Illumina software use a systematic identifier:

@HWUSI-EAS100R:6:73:941:1973#0/1

[edit] NCBI Short Read Archive

FASTQ files from the NCBI Short Read Archive often include a description, e.g.

@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
+SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC

In this example there is an NCBI assigned identifier while the description holds the original identifier from Solexa/Illumina (as described above) plus the read length.

Also note that the NCBI have converted this FASTQ data from the original Solexa/Illumina encoding to the Sanger standard (see encodings below).

[edit] Variations

[edit] Quality

A quality value Q is an integer mapping of p, the probability of the corresponding sequence letter being incorrect. It is calculated as follows:

Until version 1.2, the SolexaPipeline (the software that is delivered with the Illumina GenomeAnalyzer) used a differend mapping, encoding the odds ratio p/(1-p) instead of the probability p:

Although both mappings are asympotically identical at higher quality values, they differ at lower quality levels.

Since version 1.3, the SolexaPipeline software uses the standard formula.

[edit] Encoding

• Sanger format can encode a Phred quality score from 0 to 93 using ASCII 33 to 126 (although in raw read data the Phred quality score rarely exceeds 60, higher scores are possible in assemblies or read maps).
• Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected)
• Illumina 1.3+ format can encode a Phred quality score from 0 to 62 using ASCII 64 to 126 (although in raw read data Phred scores from 0 to 40 only are expected).

[edit] File extension

There is no standard file extension for a FASTQ file, but .fq, .fastq, and .txt are commonly used.

[edit] Format converters

• Biopython (interconverts Sanger, Solexa and Illumina 1.3+)
• EMBOSS version 6.1.0 onwards (interconverts Sanger, Solexa and Illumina 1.3+)
• Bioperl version 1.6.1 and onward will interconvert Sanger, Solexa and Illumina 1.3+.
• MAQ can convert from Solexa to Sanger (use this patch to support Illumina 1.3+ files).

[edit] See also

• FASTA format
• List of file formats for molecular biology

[edit] External links

• MAQ webpage discussing FASTQ variants