The Personal Sequence Database

Read the BMC Bioinformatics paper about the Personal Sequence Database

The Personal Sequence Database (PSD) is a public resource maintained and developed by the Center for Genome Research and Biocomputing at Oregon State University.  The PSD allows a user to:

• Store DNA or Protein sequences in a web–accessible password–protected database
• Run BLAST searches against the sequence database using a web interface
• Enroll individual sequences in weekly BLAST searches to identify new hits
• Store BLAST results indefinitely
• Extract individual sequences in a variety of standard file formats
• Store data and user–entered notes for individual sequences
• Share specific sets of sequences with public users
• Allow public users to run BLAST searches against user-defined sequence sets

	As mentioned above, each PSD sequence can be subjected to a weekly BLAST search against a variety of National Center for Biotechnology Information (NCBI) databases.  If new BLAST hits are identified, the user will receive an email alert. A user can also perform manual searches for new BLAST hits at any time. The following combinations of NCBI database and BLAST program are available:
	BLASTN or TBLASTN of non-redundant nucleotide sequences BLASTN or TBLASTN of EST sequences human mouse other BLASTN or TBLASTN of Genome Survey Sequences (GSS) BLASTN or TBLASTN of Sequence Tagged Sites (STS) BLASTP or BLASTX of non-redundant protein sequences

A user can increase the specificity of BLAST searches using E-value restrictions and NCBI Entrez terms. For example, Entrez terms can restrict a BLAST search to sequences originating from a single organism (or taxonomic group of organisms).

PSD sequences are viewed in a table format, as displayed below. Each sequence has an identifier, a short description and information about the BLAST search it is subjected to, if applicable. When new BLAST hits are present you will see 'New Hits' in the 'BLAST' column.

A list of BLAST hits can be stored for every PSD sequence, even if it is not enrolled in the BLAST tracking system. BLAST hits are listed in a table format. As illustrated below, links to NCBI are available for each BLAST hit. Links are also available to view sequence alignments between the query sequence and the sequence of the BLAST hit. New BLAST hits are accentuated by color and are easily identified in the table.

Individual PSD sequences can be retrieved in a variety of standard file formats. Additionally, sequences from the database can be bulk extraced in FASTA format.

A data page is stored for every PSD sequence entry. From the sequence data page, the user can change the sequence name, description or the primary sequence. Additionally, the user can choose the characteristics of the BLAST search. It is also from the data page that a user enrolls the sequence into the BLAST tracking system. The BLAST characteristics are entirely optional — PSD sequences need not be subjected to BLAST searches. The data page also stores information about potential protein domains, including a graphical representation of the location of identified domains and the text output from the domain search.

If you would like to sign-up to use the Personal Sequence Database, go to the online registration page. Registration is automatic and you will have immediate access to your Personal Sequence Database.