FastA Format

The official FastA documentation can be found here

FastA format is the most basic format for reporting a sequence and is accepted by almost all sequence analysis program. It only contains a sequence name, a description of the sequence (metadata, sequencer info, annotations, etc.), and the sequence itself – it can be either nucleic acids or amino acids as long as it adheres to the format.

Each sequence consists of at least two lines:

  1. The first is the sequence header, which always starts with a ‘>’
    • Everything from the beginning ‘>’ to the first whitespace is considered the sequence identifier. Everything after that is considered the sequence description (this can be metadata, machine serial number, read orientation, etc.)
  2. The sequence itself
    • Note that the sequence can span multiple lines, depending on the length of the sequence.
>Chr1 CHROMOSOME dumped from ADB: Jun/20/09 14:53; last updated: 2009-02-02
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAATCTTTAAATCCTACATCCAT
GAATCCCTAAATACCTAATTCCCTAAACCCGAAACCGGTTTCTCTGGTTGAAAATCATTGTGTATATAATGATAATTTT
ATCGTTTTTATGTAATTGCTTATTGTTGTGTGTAGATTTTTTAAAAATATCATTTGAGGTCAATACAAATCCTATTTCT
TGTGGTTTTCTTTCCTTCACTTAGCTATGGATGGTTTATCTTCATTTGTTATATTGGATACAAGCTTTGCTACGATCTA
CATTTGGGAATGTGAGTCTCTTATTGTAACCTTAGGGTTGGTTTATCTCAAGAATCTTATTAATTGTTTGGACTGTTTA
TGTTTGGACATTTATTGTCATTCTTACTCCTTTGTGGAAATGTTTGTTCTATCAATTTATCTTTTGTGGGAAAATTATT
TAGTTGTAGGGATGAAGTCTTTCTTCGTTGTTGTTACGCTTGTCATCTCATCTCTCAATGATATGGGATGGTCCTTTAG
CATTTATTCTGAAGTTCTTCTGCTTGATGATTTTATCCTTAGCCAAAAGGATTGGTGGTTTGAAGACACATCATATCAA
AAAAGCTATCGCCTCGACGATGCTCTATTTCTATCCTTGTAGCACACATTTTGGCACTCAAAAAAGTATTTTTAGATGT
TTGTTTTGCTTCTTTGAAGTAGTTTCTCTTTGCAAAATTCCTCTTTTTTTAGAGTGATTTGGATGATTCAAGACTTCTC
GGTACTGCAAAGTTCTTCCGCCTGATTAATTATCCATTTTACCTTTGTCGTAGATATTAGGTAATCTGTAAGTCAACTC
ATATACAACTCATAATTTAAAATAAAATTATGATCGACACACGTTTACACATAAAATCTGTAAATCAACTCATATACCC
GTTATTCCCACAATCATATGCTTTCTAAAAGCAAAAGTATATGTCAACAATTGGTTATAAATTATTAGAAGTTTTCCAC
TTATGACTTAAGAACTTGTGAAGCAGAAAGTGGCAACACCCCCCACCTCCCCCCCCCCCCCCCACCCCCCAAATTGAGA
AGTCAATTTTATATAATTTAATCAAATAAATAAGTTTATGGTTAAGAGTTTTTTACTCTCTTTATTTTTCTTTTTCTTT

Software that use FastA format

In most case throughout this workshop you will encounter this format when using a reference sequence. DB query tools like blast and multiple-sequence alignment algorithms accept only FastA format. Also, when you download reference genomes they are delivered in this format.

How are these files generated?

  • Some older NGS sequencers report sequences in this format. Sanger sequencing also delivers in this format.
  • Most sequence databases store sequences in FastA format which is available for download.
  • FastA can also generated from a FastQ file.

Let’s grab one!

Generally you will download a reference genome. You can find it here: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS236.genomic.fa.gz

Download it onto the cluster in a new folder in your scratch called file_formats. Unzip this and look at the size. What command would you use to open it?

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