SeqXML is an XML Schema to describe biological sequences. SeqXML is designed to be a simple and versatile format to store sequence data. The FASTA sequence format is so widely used because it is simple and versatile, but FASTA's weakness is the lack of structure in its header. The lack of standardization in FASTA headers makes it time-consuming and labor-intensive to parse header information in FASTA sequences gathered from different sources.

SeqXML solves this problem by adding just enough structure to allow easy parsing while still being a lightweight format. There are only two required fields: the id and the sequence.

If you do choose to specify additional information about the sequence, SeqXML makes it easy to do in a standardized way. The most common types of sequence metadata, such as description, species, and alternative IDs, are already encoded in SeqXML.

It's flexible, too. You can include your own metadata as properties, which can be just a tag, like "has_splice_variants", or a tag-value pair, where a named category like "prediction method" has a value like "genscan".

And XML is a markup language which makes it easy to process and validate. Using XML as the "container" for sequence data means it's possible to do some simple validation, so that common problems like duplicate entries and invalid sequence letters are detected automatically.

The document describes the content of an SeqXML file version 0.4 and gives details about each element and attribute. For more information about SeqXML, including tools to convert SeqXML to and from other sequence formats, visit seqxml.org.

In this section we walk through an example of a SeqXML file, shown here:

        <?xml version="1.0"?>
        <seqXML source="Ensembl" sourceVersion="56" speciesName="Homo sapiens" ncbiTaxID="9606" seqXMLversion="0.4">
            <entry id="A12345">
                <DNAseq>ACTGCGAAATGTGCCCGGGNNNN</DNAseq>
            </entry>
            <entry id="ENSG00000173402" source="Ensembl">
                <species name="Homo sapiens" ncbiTaxID="9606"/>
                <description>dystroglycan 1</description>
                <RNAseq>AAGGC----UGAUGUC.....ACAU</RNAseq>
                <DBRef source="RefSeq" id="NM_004393"/>
                <property name="prediction_method" value="manual curation"/>
                <property name="has_splice_variants"/>
            </entry>
            <entry id="ENSG000001734023" source="Ensembl">
                <description>example description.</description>
                <AAseq>AAGGCGAAA----AA*AAAAAGT.....CACJOXA</AAseq>
            </entry>
            <entry id="ENSG0000017340233">
                <description>another example description</description>
                <DNAseq>AAGGCGTTAAA----AAAAAAAGT.....CACTA</DNAseq>
            </entry>
        </seqXML>

The root element in the XML file is the seqXML tag. It indicates the version of SeqXML used, and optionally the origin of the data (often, a database like Ensembl or Swiss-Prot) and the version of that database. The optional attributes speciesName and ncbiTaxID define the species of origin of all entries. Here you can see this SeqXML file contains records from Human from Ensembl version 56:

        <seqXML source="Ensembl" sourceVersion="56" speciesName="Homo sapiens" ncbiTaxID="9606" seqXMLversion="0.4">

Under the seqXML tag there are four entries, one entry for each sequence. The first entry shows the minimum necessary. It's just an identifier and a sequence:

        <entry id="A12345">
            <DNAseq>ACTGCGAAATGTGCCCGGGNNNN</DNAseq>
        </entry>

Note that the type of sequence is specified by the sequence tag used. Here, it's <DNAseq> to indicate a DNA alphabet. The other options are RNAseq and AAseq for RNA and amino acid alphabets, respectively. If you validate a SeqXML file, the sequence will be checked to make sure it contains only IUPAC-allowed characters for that sequence type.

The second entry is much more detailed:

        <entry id="ENSG00000173402" source="Ensembl">
            <RNAseq>AAGGC----UGAUGUC.....ACAU</RNAseq>
            <description>dystroglycan 1</description>
            <species name="Homo sapiens" ncbiTaxID="9606"/>
            <DBRef source="RefSeq" id="NM_004393"/>
            <property name="has_splice_variants"/>
            <property name="prediction_method" value="manual curation"/>
        </entry>

In addition to the ID and the sequence (an RNA sequence in this case), there are several other pieces of optional information. There's an optional source attribute identifying the ID as being an Ensembl ID. There's also a description, a local species definition, a database cross-reference and its source (RefSeq in this case), and then a couple of properties.

Rather than overloading the description field, as has become common with FASTA records, properties are a way to include additional information related to the sequence. Properties can be written in two ways. First, as simply a tag, and secondly as a tag and associated value. The example here shows one of each:

         <property name="has_splice_variants"/>
         <property name="prediction_method" value="manual curation"/>

Of course these simple tags cannot properly represent more complicated types of metadata, such as journal references, but they are not intended to. SeqXML is designed as a lightweight format, not as a comprehensive one. For that purpose, there are other more appropriate XML sequence data formats, such as UniProt XML or EMBL XML.

So that's a quick overview of SeqXML. Tools for using it and converting to and from other sequence formats are available at SeqXML.org. A more detailed reference documentation continues below.