56 lines
1.4 KiB
ReStructuredText
56 lines
1.4 KiB
ReStructuredText
File formats usable with OBITools
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=================================
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.. _the-sequence-files:
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The sequence files
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------------------
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Sequences can be stored following various format. OBITools knows
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some of them. The central format for sequence files manipulated by OBITools scripts
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is the :doc:`fasta format <fasta>`. OBITools extends the fasta format by specifying
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a syntax to include in the definition line data qualifying the sequence.
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All file formats use the :doc:`IUPAC <iupac>` code for encoding nucleotides and
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amino-acids.
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.. toctree::
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:maxdepth: 2
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iupac
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fasta
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fastq
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attributes
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genbank
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embl
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The taxonomy files
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------------------
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Many OBITools are able to take into account taxonomic data. This is done in general by specifying
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either a directory containing all :doc:`NCBI taxonomy dump files <./taxdump>` or an
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:doc:`obitaxonomy <./obitaxonomy>` formatted database.
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.. toctree::
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:maxdepth: 2
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taxdump
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obitaxonomy
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The ecoPCR files
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----------------
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ecoPCR_ simulates a PCR experiment by selecting in a sequence database, sequences matching
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simultaneously two primers sequences in a way allowing a PCR amplification of a DNA region.
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The ecoPrimers files
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--------------------
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The OBITools files
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------------------
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.. _ecoPCR: http://www.grenoble.prabi.fr/trac/ecoPCR
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.. _LECA: http://www-leca.ujf-grenoble.fr
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.. _`NCBI taxonomy`: http://www.ncbi.nlm.nih.gov/taxonomy |