PEFF:A Common Sequence Database Format in Proteomics is now available for Public Comment on the PSI Web site (http://psidev.info/index.php?q=node/363). The public comment period enables the wider community to provide feedback on a proposed standard before it is formally accepted, and thus is an important step in the standardisation process.
This document presents a unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc). This format enables consistent extraction, display and processing of information such as protein/nucleotide sequence database entry identifier, description, taxonomy, etc. across software platforms. It also allows the representation of structural annotations such as post-translational modifications, mutations and other processing events. The proposed format has the form of a flat file that extends the formalism of the individual sequence entries as presented in a FASTA format and that includes a header of meta data to describe relevant information about the database(s) from which the sequence has been obtained (i.e., name, version, etc). The format is named PEFF (PSI Extended FASTA Format). Sequence database providers are encouraged to generate this format as part of their release policy or to provide appropriate converters that can be incorporated into processing tools.
This is an announcement to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but know someone who may be, please consider alerting them towards this information. There is no requirement that people commenting should have had any prior contact with the PSI