There is no standard file extension for a text file containing FASTA formatted sequences. The following sequence('>') identifiers now refer to the species genome of the respective orthologous sequences: The group('>') identifier typically refers to the target gene regulated by the hidden motif in the dataset. The word following the '>' symbol is further called the group identifier, optionally followed by a tab-spaced more detailed description. Sets of orthologous sequences (regulating the same target genes in different species) are separated by a line consisting of a double greater-than ('>') symbol in the first column. The sequence identifier typically refers to the target gene regulated by the hidden motif in the dataset:įor orthologous DNA sequences from multiple species (input for PHMS and NOMS): The sequence data starts on the next line following the text line and ends if another line starting with a ">" appears this indicates the start of another sequence. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is a description (optional) separated from the identifier by a white space or tab.
The identifier description line is distinguished from the sequence data by a greater-than ('>') symbol in the first column. The format also allows for sequence names and comments to precede the sequences.Ī sequence in FASTA format begins with a single-line identifier description, followed by lines of DNA sequence data. In bioinformatics, FASTA format is a text-based format for representing DNA sequences, in which base pairs are represented using a single-letter code where A=Adenosine, C=Cytosine, G=Guanine, T=Thymidine and N= any of A,C,G,T. In MotifSuite, a FASTA file is supplied as input for MotifSampler, PhyloMotifSampler, NOrthoMotifSampler, MotifLocator, CreateBackgroundModel. We comment on all optional and required fields in case you need to supply such a file as input to MotifSuite. This page describes the format of a file that describes a set of DNA sequences from one species, or sets of orthologous sequences from multiple species in FASTA format.
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